2E2H

RNA polymerase II elongation complex at 5 mM Mg2+ with GTP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth A]	d2e2ha1	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta-prime	RBP1	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E [auth B]	d2e2hb1	Multi-domain proteins (alpha and beta)	beta and beta-prime subunits of DNA dependent RNA-polymerase	beta and beta-prime subunits of DNA dependent RNA-polymerase	RNA-polymerase beta	RBP2	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F [auth C]	d2e2hc1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RNA polymerase alpha subunit dimerisation domain	RPB3	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F [auth C]	d2e2hc2	Alpha and beta proteins (a+b)	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	Insert subdomain of RNA polymerase alpha subunit	RPB3	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G [auth E]	d2e2he1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Eukaryotic RPB5 N-terminal domain	Eukaryotic RPB5 N-terminal domain	Eukaryotic RPB5 N-terminal domain	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G [auth E]	d2e2he2	Alpha and beta proteins (a+b)	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit	RPB5	Eukaryotic RPB5 C-terminal domain	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
H [auth F]	d2e2hf1	All alpha proteins	RPB6/omega subunit-like	RPB6/omega subunit-like	RPB6	RPB6	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
I [auth H]	d2e2hh1	All beta proteins	OB-fold	Nucleic acid-binding proteins	RNA polymerase subunit RBP8	RNA polymerase subunit RBP8	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
J [auth I]	d2e2hi1	Small proteins	Rubredoxin-like	Zinc beta-ribbon	Transcriptional factor domain	RBP9 subunit of RNA polymerase II	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
K [auth J]	d2e2hj1	All alpha proteins	DNA/RNA-binding 3-helical bundle	RNA polymerase subunit RPB10	RNA polymerase subunit RPB10	RNA polymerase subunit RPB10	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
L [auth K]	d2e2hk1	Alpha and beta proteins (a+b)	DCoH-like	RBP11-like subunits of RNA polymerase	RBP11/RpoL	RPB11	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
M [auth L]	d2e2hl1	Small proteins	Rubredoxin-like	RNA polymerase subunits	RBP12 subunit of RNA polymerase II	RBP12 subunit of RNA polymerase II	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth A]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8042682	3001330	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8042684	3001330	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8042685	3001655	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8042687	3001500	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	Eukaryotic RPB5 N-terminal domain	8044454	3000444	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	RPB5-like RNA polymerase subunit	8035939	3001722	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	RPB6/omega subunit-like	8042688	3000189	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8041967	3002702	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8093392	3002702	SCOP2B (2022-06-29)
J [auth I]	SCOP2B Superfamily	Zinc beta-ribbon	8042689	3001238	SCOP2B (2022-06-29)
J [auth I]	SCOP2B Superfamily	Zinc beta-ribbon	8042690	3001238	SCOP2B (2022-06-29)
K [auth J]	SCOP2B Superfamily	RNA polymerase subunit RPB10	8042692	3001213	SCOP2B (2022-06-29)
L [auth K]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8042694	3001655	SCOP2B (2022-06-29)
M [auth L]	SCOP2B Superfamily	RNA polymerase subunits	8042695	3001823	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth A]	RNA_pol_Rpb1_2	e2e2hA5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
D [auth A]	RNA_pol_Rpb1_2_1	e2e2hA2	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: RNA_pol_Rpb1_2_1	ECOD (1.6)
D [auth A]	RNA_pol_Rpb1_7	e2e2hA8	A: a+b two layers	X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_7	ECOD (1.6)
D [auth A]	RNA_pol_Rpb1_7_1	e2e2hA6	A: a+b two layers	X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_7_1	ECOD (1.6)
D [auth A]	RNA_pol_Rpb1_1	e2e2hA4	A: a+b complex topology	X: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	T: N-terminal domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_1	ECOD (1.6)
D [auth A]	RNA_pol_Rpb1_5_3rd	e2e2hA1	A: a+b complex topology	X: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: central helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_5_3rd	ECOD (1.6)
D [auth A]	RNA_pol_Rpb1_6	e2e2hA7	A: a+b complex topology	X: helical domain in yeast RNA-polymerases	H: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology)	T: third helical domain in yeast RNA-polymerase II beta-prime subunit	F: RNA_pol_Rpb1_6	ECOD (1.6)
D [auth A]	RNA_pol_Rpb1_4	e2e2hA3	A: a+b complex topology	X: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: second helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_4	ECOD (1.6)
D [auth A]	RNA_pol_Rpb1_3	e2e2hA9	A: a+b complex topology	X: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: first helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_3	ECOD (1.6)
E [auth B]	RNA_pol_Rpb2_6_3rd_2	e2e2hB3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_2	ECOD (1.6)
E [auth B]	RNA_pol_Rpb2_6_2nd_1	e2e2hB5	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb2_6_2nd_1	ECOD (1.6)
E [auth B]	RNA_pol_Rpb2_3	e2e2hB4	A: a+b complex topology	X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_3	ECOD (1.6)
E [auth B]	RNA_pol_Rpb2_1	e2e2hB2	A: a+b complex topology	X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: insertion domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_1	ECOD (1.6)
E [auth B]	RNA_pol_Rpb2_45_1	e2e2hB1	A: a+b complex topology	X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: barrel domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_45_1	ECOD (1.6)
E [auth B]	RNA_pol_Rpb2_7	e2e2hB21	A: a+b complex topology	X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_7	ECOD (1.6)
E [auth B]	RNA_pol_Rpb2_4	e2e2hB6	A: a+b complex topology	X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	T: inserted a+b domain in yeast RNA polymerase beta subunit	F: RNA_pol_Rpb2_4	ECOD (1.6)
F [auth C]	RNA_pol_L_1	e2e2hC1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_1	ECOD (1.6)
F [auth C]	RNA_pol_A_bac_1	e2e2hC2	A: a+b complex topology	X: Ribosomal protein TL5/L25 C-terminal domain-like	H: Insert subdomain of RNA polymerase alpha subunit (From Topology)	T: Insert subdomain of RNA polymerase alpha subunit	F: RNA_pol_A_bac_1	ECOD (1.6)
G [auth E]	RNA_pol_Rpb5_C	e2e2hE1	A: a+b two layers	X: RPB5-like RNA polymerase subunit (From Topology)	H: RPB5-like RNA polymerase subunit (From Topology)	T: RPB5-like RNA polymerase subunit	F: RNA_pol_Rpb5_C	ECOD (1.6)
G [auth E]	RNA_pol_Rpb5_N	e2e2hE2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Eukaryotic RPB5 N-terminal domain (From Topology)	T: Eukaryotic RPB5 N-terminal domain	F: RNA_pol_Rpb5_N	ECOD (1.6)
H [auth F]	RNA_pol_Rpb6_1	e2e2hF1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RPB6	F: RNA_pol_Rpb6_1	ECOD (1.6)
I [auth H]	RNA_pol_Rpb8	e2e2hH1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: RNA_pol_Rpb8	ECOD (1.6)
J [auth I]	RNA_POL_M_15KD	e2e2hI1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: RNA_POL_M_15KD	ECOD (1.6)
J [auth I]	TFIIS_C	e2e2hI2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: TFIIS_C	ECOD (1.6)
K [auth J]	RNA_pol_N	e2e2hJ1	A: alpha arrays	X: HTH	H: RPB10 (From Topology)	T: RPB10	F: RNA_pol_N	ECOD (1.6)
L [auth K]	RNA_pol_L_2	e2e2hK1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_2	ECOD (1.6)
M [auth L]	DNA_RNApol_7kD	e2e2hL1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: DNA_RNApol_7kD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth A]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
D [auth A]	3.30.1490.180	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D [auth A]	1.10.274.100	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (4.3.0)
D [auth A]	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.3.0)
D [auth A]	3.30.1360.140	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
E [auth B]	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
E [auth B]	3.90.1070.20	Alpha Beta	Alpha-Beta Complex	Hypothetical Protein Ta0175	Chain: A, domain 2	CATH (4.3.0)
E [auth B]	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.3.0)
E [auth B]	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
E [auth B]	3.90.1800.10	Alpha Beta	Alpha-Beta Complex	DCoH-like	RNA polymerase alpha subunit dimerisation domain	CATH (4.3.0)
F [auth C]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
F [auth C]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.3.0)
G [auth E]	3.40.1340.10	Alpha Beta	3-Layer(aba) Sandwich	Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide	Chain: A	CATH (4.3.0)
G [auth E]	3.90.940.20	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RPB5-like RNA polymerase subunit	CATH (4.3.0)
H [auth F]	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.3.0)
I [auth H]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
J [auth I]	2.20.25.10	Mainly Beta	Single Sheet	N-terminal domain of TfIIb		CATH (4.3.0)
K [auth J]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
L [auth K]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
M [auth L]	2.20.28.30	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	RNA polymerase ii, chain L	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A]	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
D [auth A]	PF04990	RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7)	RNA polymerase Rpb1, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile modu ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [1,2].	Domain
D [auth A]	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
D [auth A]	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
D [auth A]	PF04992	RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6)	RNA polymerase Rpb1, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile modu ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2]. This family appears to be specific to the largest subunit of RNA polymerase II.	Domain
D [auth A]	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
D [auth A]	PF04997	RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)	RNA polymerase Rpb1, domain 1	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp dom ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].	Domain
E [auth B]	PF04561	RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)	RNA polymerase Rpb2, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).	Domain
E [auth B]	PF04560	RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)	RNA polymerase Rpb2, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].	Domain
E [auth B]	PF04565	RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)	RNA polymerase Rpb2, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].	Domain
E [auth B]	PF04566	RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4)	RNA polymerase Rpb2, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain [1].	Domain
E [auth B]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
E [auth B]	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
E [auth B]	PF04567	RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)	RNA polymerase Rpb2, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain [1].	Domain
F [auth C]	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.	Domain
F [auth C]	PF01000	RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)	RNA polymerase Rpb3/RpoA insert domain	Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal	Domain
G [auth E]	PF01191	RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)	RNA polymerase Rpb5, C-terminal domain	The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.	Domain
G [auth E]	PF03871	RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N)	RNA polymerase Rpb5, N-terminal domain	Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ...	Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [3]. This module is important for positioning the downstream DNA.	Domain
H [auth F]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
I [auth H]	PF03870	RNA polymerase Rpb8 (RNA_pol_Rpb8)	RNA polymerase Rpb8	-	Family
J [auth I]	PF02150	RNA polymerases M/15 Kd subunit (Zn_ribbon_RPB9)	RNA polymerases M/15 Kd subunit		Domain
J [auth I]	PF01096	Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)	Transcription factor S-II (TFIIS)		Domain
K [auth J]	PF01194	RNA polymerases N / 8 kDa subunit (RNA_pol_N)	RNA polymerases N / 8 kDa subunit		Domain
L [auth K]	PF13656	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11.	Domain
M [auth L]	PF03604	DNA directed RNA polymerase, 7 kDa subunit (Zn_ribbon_RPAB4)	DNA directed RNA polymerase, 7 kDa subunit		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth R]	5'-R(APUPCPGPAPGPAPGPGPA)-3'	-	-	-
B [auth T]	28-MER DNA template strand	-	-	-
C [auth N]	5'-D(CPTPGPCPTPTPAPTPCPGPGPTPAPG)-3'	-	-	-
D [auth A]	DNA-directed RNA polymerase II largest subunit	DNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process translesion synthesis cellular response to stimulus postreplication repair response to stimulus DNA metabolic process DNA synthesis involved in DNA repair cellular response to stress DNA damage response response to stress DNA biosynthetic process DNA repair RNA-templated transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm RNA polymerase II, core complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
E [auth B]	DNA-directed RNA polymerase II 140 kDa polypeptide	ribonucleoside binding binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding DNA binding nucleic acid binding RNA binding mRNA binding cation binding ion binding metal ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process cellular process macromolecule metabolic process RNA-templated transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle supramolecular complex cytoplasmic stress granule RNA polymerase II, holoenzyme protein-containing complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen nucleoplasm RNA polymerase II, core complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
F [auth C]	DNA-directed RNA polymerase II 45 kDa polypeptide	DNA binding binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding protein dimerization activity DNA binding binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups protein binding protein dimerization activity cation binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II termination of RNA polymerase II transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
G [auth E]	DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide	DNA binding binding nucleic acid binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III nucleolar large rRNA transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex
H [auth F]	DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide	DNA binding binding nucleic acid binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III nucleolar large rRNA transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex cytoplasm
I [auth H]	DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide	DNA binding binding nucleic acid binding	nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription nucleolar large rRNA transcription by RNA polymerase I RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription transcription by RNA polymerase III DNA-templated transcription initiation transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex
J [auth I]	DNA-directed RNA polymerase II subunit 9	binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process DNA-templated transcription initiation DNA-templated transcription transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation maintenance of transcriptional fidelity during transcription elongation maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II cellular response to stimulus response to stimulus transcription-coupled nucleotide-excision repair DNA metabolic process cellular response to stress nucleotide-excision repair DNA damage response response to stress DNA repair	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen RNA polymerase II, holoenzyme protein-containing complex nuclear protein-containing complex transferase complex nucleoplasm RNA polymerase II, core complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex
K [auth J]	DNA-directed RNA polymerases I/II/III subunit 10	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III nucleolar large rRNA transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I transcription initiation at RNA polymerase I promoter	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure membraneless organelle catalytic complex intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex
L [auth K]	DNA-directed RNA polymerase II 13.6 kDa polypeptide	DNA binding binding nucleic acid binding protein binding protein dimerization activity	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process DNA-templated transcription termination DNA-templated transcription transcription by RNA polymerase II termination of RNA polymerase II transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
M [auth L]	DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process metabolic process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III nucleolar large rRNA transcription by RNA polymerase I transcription by RNA polymerase I rRNA transcription rRNA metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I transcription initiation at RNA polymerase I promoter	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen protein-containing complex RNA polymerase I complex nuclear protein-containing complex transferase complex catalytic complex transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex cytoplasm peroxisome microbody

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
D [auth A]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D [auth A]	IPR007075	RNA polymerase Rpb1, domain 6	Domain
D [auth A]	IPR000684	RNA polymerase II, heptapeptide repeat, eukaryotic	Repeat
D [auth A]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
D [auth A]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
D [auth A]	IPR006592	RNA polymerase, N-terminal	Domain
D [auth A]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
D [auth A]	IPR007073	RNA polymerase Rpb1, domain 7	Domain
D [auth A]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
D [auth A]	IPR038593	RNA polymerase Rpb1, domain 7 superfamily	Homologous Superfamily
D [auth A]	IPR000722	RNA polymerase, alpha subunit	Domain
D [auth A]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
D [auth A]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
E [auth B]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
E [auth B]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
E [auth B]	IPR007646	RNA polymerase Rpb2, domain 4	Domain
E [auth B]	IPR007647	RNA polymerase Rpb2, domain 5	Domain
E [auth B]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
E [auth B]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
E [auth B]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
E [auth B]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
E [auth B]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
E [auth B]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
E [auth B]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
E [auth B]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
F [auth C]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
F [auth C]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
F [auth C]	IPR050518	Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase Subunit	Family
F [auth C]	IPR022842	DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1	Family
F [auth C]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
F [auth C]	IPR001514	DNA-directed RNA polymerase, 30-40kDa subunit, conserved site	Conserved Site
F [auth C]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
G [auth E]	IPR036710	RNA polymerase Rpb5, N-terminal domain superfamily	Homologous Superfamily
G [auth E]	IPR014381	DNA-directed RNA polymerase subunit Rpo5/Rpb5	Family
G [auth E]	IPR035913	RPB5-like RNA polymerase subunit superfamily	Homologous Superfamily
G [auth E]	IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	Domain
G [auth E]	IPR020608	RNA polymerase, subunit H/Rpb5, conserved site	Conserved Site
G [auth E]	IPR005571	RNA polymerase, Rpb5, N-terminal	Domain
H [auth F]	IPR028363	DNA-directed RNA polymerase, subunit RPB6	Family
H [auth F]	IPR006111	Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit	Family
H [auth F]	IPR020708	DNA-directed RNA polymerase, 14-18kDa subunit, conserved site	Conserved Site
H [auth F]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
H [auth F]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
I [auth H]	IPR005570	DNA-directed RNA polymerases I, II, and III subunit RPABC3	Family
I [auth H]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
J [auth I]	IPR001529	DNA-directed RNA polymerase II subunit RPB9-like, zinc ribbon	Domain
J [auth I]	IPR012164	DNA-directed RNA polymerase subunit/transcription factor S	Family
J [auth I]	IPR001222	Zinc finger, TFIIS-type	Domain
J [auth I]	IPR034012	Pol II subunit B9, C-terminal zinc ribbon	Domain
J [auth I]	IPR019761	DNA-directed RNA polymerase M, 15kDa subunit, conserved site	Conserved Site
K [auth J]	IPR020789	RNA polymerases, subunit N, zinc binding site	Binding Site
K [auth J]	IPR000268	DNA-directed RNA polymerase subunit RPABC5/Rpb10	Family
K [auth J]	IPR023580	RNA polymerase subunit RPB10	Homologous Superfamily
L [auth K]	IPR009025	DNA-directed RNA polymerase, RBP11-like dimerisation domain	Domain
L [auth K]	IPR037685	RNA polymerase RBP11	Family
L [auth K]	IPR022905	DNA-directed RNA polymerase subunit Rpo11-like	Family
L [auth K]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
L [auth K]	IPR008193	DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site	Conserved Site
M [auth L]	IPR006591	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	Family
M [auth L]	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
M [auth L]	IPR039747	DNA-directed RNA polymerases I, II, and III subunit RPABC4	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
D [auth A], E [auth B]	DNA-directed RNA polymerase M-CSA #788	DNA-dependent RNA polymerases bind to promoter DNA in transcription initiation, opens the duplex strands, and can convert from initiation to elongation phase conformation. More specifically, RNA polymerase II transcribes mRNA in the nucleus of eukaryotes, with closely related enzymes in bacteria and some viruses. RNA synthesis occurs through cycles of repeated ribonucleotide incorporation. While RNAPII is apart of a family containing multiple subunits, there are also single subunit RNAPs such as in the T7 bacteriophage which display high similarity to DNA polymerases.	Defined by 5 residues: ASP:D-481 [auth A-481]ASP:D-483 [auth A-483]ASP:D-485 [auth A-485]HIS:D-1085 [auth A-1085]ASP:E-837 [auth B-837] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.7.7.6 (PDB Primary Data) Search M-CSA Motif + EC 2.7.7.6