Annotations: 6ZFB

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth D]	SCOP2B Superfamily	Winged helix DNA-binding domain	8103637	3000034	SCOP2B (2022-06-29)
H [auth d]	SCOP2B Superfamily	Winged helix DNA-binding domain	8103637	3000034	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)
I [auth e]	DUF1447	e6zfbe1	A: a+b two layers	X: GP2-like	H: Bacterial RNA polymerase subunit epsilon (From Topology)	T: Bacterial RNA polymerase subunit epsilon	F: DUF1447	ECOD (1.6)
B [auth E]	DUF1447	e6zfbE1	A: a+b two layers	X: GP2-like	H: Bacterial RNA polymerase subunit epsilon (From Topology)	T: Bacterial RNA polymerase subunit epsilon	F: DUF1447	ECOD (1.6)
J [auth u]	RNA_pol_L	e6zfbu1	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	ECOD (1.6)
J [auth u]	RNA_pol_A_bac	e6zfbu2	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	ECOD (1.6)
C [auth U]	RNA_pol_L	e6zfbU2	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	ECOD (1.6)
C [auth U]	RNA_pol_A_bac	e6zfbU1	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	ECOD (1.6)
D [auth V]	RNA_pol_L	e6zfbV1	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	ECOD (1.6)
D [auth V]	RNA_pol_A_bac	e6zfbV2	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	ECOD (1.6)
K [auth v]	RNA_pol_L	e6zfbv2	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	ECOD (1.6)
K [auth v]	RNA_pol_A_bac	e6zfbv1	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	ECOD (1.6)
E [auth X]	RNA_pol_Rpb2_6_3rd_1	e6zfbX5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_1	ECOD (1.6)
E [auth X]	RNA_pol_Rpb2_6_2nd	e6zfbX1	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	ECOD (1.6)
E [auth X]	RNA_pol_Rpb2_6_1st	e6zfbX4	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_1st	ECOD (1.6)
E [auth X]	RNA_pol_Rpb2_3	e6zfbX2	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 X]	RNA_pol_Rpb2_1	e6zfbX3	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 X]	RNA_pol_Rpb2_45	e6zfbX6	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	ECOD (1.6)
E [auth X]	RNA_pol_Rpb2_7	e6zfbX7	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)
L [auth x]	RNA_pol_Rpb2_6_3rd_1	e6zfbx6	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_1	ECOD (1.6)
L [auth x]	RNA_pol_Rpb2_6_2nd	e6zfbx5	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	ECOD (1.6)
L [auth x]	RNA_pol_Rpb2_6_1st	e6zfbx1	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_1st	ECOD (1.6)
L [auth x]	RNA_pol_Rpb2_3	e6zfbx7	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)
L [auth x]	RNA_pol_Rpb2_1	e6zfbx3	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)
L [auth x]	RNA_pol_Rpb2_45	e6zfbx4	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	ECOD (1.6)
L [auth x]	RNA_pol_Rpb2_7	e6zfbx2	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)
F [auth Y]	RNA_pol_Rpb1_2	e6zfbY3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
F [auth Y]	PRK00566_1st	e6zfbY6	A: alpha arrays	X: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	H: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	T: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit	F: PRK00566_1st	ECOD (1.6)
F [auth Y]	PRK00566_2nd	e6zfbY7	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: PRK00566_2nd	ECOD (1.6)
F [auth Y]	RNA_pol_Rpb1_5_2nd	e6zfbY8	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_Rpb1_5_2nd	ECOD (1.6)
F [auth Y]	RNA_pol_Rpb1_1	e6zfbY1	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)
F [auth Y]	RNA_pol_Rpb1_5_3rd	e6zfbY2	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)
F [auth Y]	RNA_pol_Rpb1_4	e6zfbY4	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)
F [auth Y]	RNA_pol_Rpb1_3	e6zfbY5	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)
M [auth y]	RNA_pol_Rpb1_2	e6zfby3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
M [auth y]	PRK00566_1st	e6zfby6	A: alpha arrays	X: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	H: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	T: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit	F: PRK00566_1st	ECOD (1.6)
M [auth y]	PRK00566_2nd	e6zfby7	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: PRK00566_2nd	ECOD (1.6)
M [auth y]	RNA_pol_Rpb1_5_2nd	e6zfby8	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_Rpb1_5_2nd	ECOD (1.6)
M [auth y]	RNA_pol_Rpb1_1	e6zfby1	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)
M [auth y]	RNA_pol_Rpb1_5_3rd	e6zfby2	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)
M [auth y]	RNA_pol_Rpb1_4	e6zfby4	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)
M [auth y]	RNA_pol_Rpb1_3	e6zfby5	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth u]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (utative)
E [auth X]	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (utative)
L [auth x]	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (utative)
F [auth Y]	1.10.274.100	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (utative)
F [auth Y]	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (utative)
M [auth y]	1.10.274.100	Mainly Alpha	Orthogonal Bundle	Enzyme I	Chain A, domain 2	CATH (utative)
M [auth y]	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (utative)
N [auth h]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
G [auth H]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], H [auth d]	PF05066	HB1, ASXL, restriction endonuclease HTH domain (HARE-HTH)	HB1, ASXL, restriction endonuclease HTH domain	-	Family
B [auth E], I [auth e]	PF07288	RNA polymerase epsilon subunit (RpoY)	RNA polymerase epsilon subunit	RNA polymerase in bacteria is a multisubunit protein complex that is essential for gene expression. This entry represents the epsilon subunit encoded by the rpoY gene. The structure of epsilon shows simple beta sheet with an alpha helix running diago ...	RNA polymerase in bacteria is a multisubunit protein complex that is essential for gene expression. This entry represents the epsilon subunit encoded by the rpoY gene. The structure of epsilon shows simple beta sheet with an alpha helix running diagonally along the back of the structure forming a beta-beta-alpha-beta fold [1].	Domain
C [auth U], D [auth V], J [auth u], K [auth v]	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
C [auth U], D [auth V], J [auth u], K [auth v]	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
E [auth X], L [auth x]	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 X], L [auth x]	PF10385	RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)	RNA polymerase beta subunit external 1 domain	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between ...	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [1].	Domain
E [auth X], L [auth x]	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 X], L [auth x]	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 X], L [auth x]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
E [auth X], L [auth x]	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
F [auth Y], M [auth y]	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
F [auth Y], M [auth y]	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
F [auth Y], M [auth y]	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
F [auth Y], M [auth y]	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
G [auth H], N [auth h]	PF13538	UvrD-like helicase C-terminal domain (UvrD_C_2)	UvrD-like helicase C-terminal domain	This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.	Domain
G [auth H], N [auth h]	PF00580	UvrD/REP helicase N-terminal domain (UvrD-helicase)	UvrD/REP helicase N-terminal domain	The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near t ...	The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D], H [auth d]	DNA-directed RNA polymerase subunit delta	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	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
B [auth E], I [auth e]	RNA polymerase subunit omega	DNA binding binding nucleic acid binding	-	cellular anatomical structure nucleoid intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
C [auth U], D [auth V], J [auth u], K [auth v]	DNA-directed RNA polymerase subunit alpha	DNA binding binding nucleic acid binding protein binding protein dimerization activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
E [auth X], L [auth x]	DNA-directed RNA polymerase subunit beta	DNA binding binding nucleic acid binding ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	response to stimulus response to chemical response to antibiotic	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
F [auth Y], M [auth y]	DNA-directed RNA polymerase subunit beta'	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding transition metal ion binding zinc ion binding	response to stimulus response to chemical response to antibiotic	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
G [auth H], N [auth h]	DNA helicase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA DNA translocase activity catalytic activity, acting on a nucleic acid chromatin extrusion motor activity catalytic activity ATP-dependent activity DNA binding nucleic acid binding ATP-dependent H3-H4 histone complex chaperone activity catalytic activity, acting on a protein histone chaperone activity ATP-dependent chromatin remodeler activity H3-H4 histone complex chaperone activity protein carrier chaperone ATP-dependent histone chaperone activity molecular carrier activity DNA helicase activity single-stranded 3'-5' DNA helicase activity single-stranded DNA helicase activity helicase activity 3'-5' DNA helicase activity cohesin loader activity DNA clamp loader activity four-way junction helicase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides ATP-dependent H2AZ histone chaperone activity forked DNA-dependent helicase activity double-stranded DNA helicase activity	cellular response to stimulus response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process DNA repair	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D], H [auth d]	IPR029757	DNA-directed RNA polymerase subunit delta	Family
A [auth D], H [auth d]	IPR038087	DNA-directed RNA polymerase subunit delta, N-terminal domain superfamily	Homologous Superfamily
A [auth D], H [auth d]	IPR007759	ASXL, HARE-HTH domain	Domain
B [auth E], I [auth e]	IPR009907	RNA polymerase epsilon subunit	Family
C [auth U], D [auth V], J [auth u], K [auth v]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
C [auth U], D [auth V], J [auth u], K [auth v]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
C [auth U], D [auth V], J [auth u], K [auth v]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
C [auth U], D [auth V], J [auth u], K [auth v]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
C [auth U], D [auth V], J [auth u], K [auth v]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
C [auth U], D [auth V], J [auth u], K [auth v]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
E [auth X], L [auth x]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
E [auth X], L [auth x]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
E [auth X], L [auth x]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
E [auth X], L [auth x]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
E [auth X], L [auth x]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
E [auth X], L [auth x]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
E [auth X], L [auth x]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
E [auth X], L [auth x]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
E [auth X], L [auth x]	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
E [auth X], L [auth x]	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
E [auth X], L [auth x]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
E [auth X], L [auth x]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
F [auth Y], M [auth y]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
F [auth Y], M [auth y]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
F [auth Y], M [auth y]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
F [auth Y], M [auth y]	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
F [auth Y], M [auth y]	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
F [auth Y], M [auth y]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
F [auth Y], M [auth y]	IPR000722	RNA polymerase, alpha subunit	Domain
F [auth Y], M [auth y]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
F [auth Y], M [auth y]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
F [auth Y], M [auth y]	IPR006592	RNA polymerase, N-terminal	Domain
F [auth Y], M [auth y]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
G [auth H], N [auth h]	IPR027785	UvrD-like helicase C-terminal domain	Domain
G [auth H], N [auth h]	IPR014016	UvrD-like helicase, ATP-binding domain	Domain
G [auth H], N [auth h]	IPR000212	DNA helicase, UvrD/REP type	Family
G [auth H], N [auth h]	IPR048228	RNA polymerase recycling motor HelD-like, bacillota	Family
G [auth H], N [auth h]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily