3EQL | pdb_00003eql

Crystal structure of the T. Thermophilus RNA polymerase holoenzyme in complex with antibiotic myxopyronin

External Resource: Annotation


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
L [auth P]d3eqlp2 All alpha proteins DNA/RNA-binding 3-helical bundle Sigma3 and sigma4 domains of RNA polymerase sigma factors Sigma3 domain Sigma70 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
L [auth P]d3eqlp3 All alpha proteins DNA/RNA-binding 3-helical bundle Sigma3 and sigma4 domains of RNA polymerase sigma factors Sigma4 domain Sigma70 (SigA, RpoD) (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
L [auth P]d3eqlp1 All alpha proteins Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors Sigma70 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Fd3eqlf2 All alpha proteins DNA/RNA-binding 3-helical bundle Sigma3 and sigma4 domains of RNA polymerase sigma factors Sigma3 domain Sigma70 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Fd3eqlf3 All alpha proteins DNA/RNA-binding 3-helical bundle Sigma3 and sigma4 domains of RNA polymerase sigma factors Sigma4 domain Sigma70 (SigA, RpoD) (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Fd3eqlf1 All alpha proteins Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors Sigma2 domain of RNA polymerase sigma factors Sigma70 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
K [auth O]d3eqlo_ All alpha proteins RPB6/omega subunit-like RPB6/omega subunit-like RNA polymerase omega subunit RNA polymerase omega subunit (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Ed3eqle_ All alpha proteins RPB6/omega subunit-like RPB6/omega subunit-like RNA polymerase omega subunit RNA polymerase omega subunit (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
J [auth N]d3eqln_ 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 RNA-polymerase beta-prime (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Dd3eqld_ 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 RNA-polymerase beta-prime (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
I [auth M]d3eqlm_ 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 automated matches (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Cd3eqlc_ 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 automated matches (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
H [auth L]d3eqll1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RNA polymerase alpha (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
H [auth L]d3eqll2 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 RNA polymerase alpha subunit (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
G [auth K]d3eqlk1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RNA polymerase alpha (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
G [auth K]d3eqlk2 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 RNA polymerase alpha subunit (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Bd3eqlb1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RNA polymerase alpha (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Bd3eqlb2 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 RNA polymerase alpha subunit (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Ad3eqla1 Alpha and beta proteins (a+b) DCoH-like RBP11-like subunits of RNA polymerase RNA polymerase alpha subunit dimerisation domain RNA polymerase alpha (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Ad3eqla2 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 RNA polymerase alpha subunit (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
L [auth P]SCOP2B SuperfamilySigma factor domain-like 8039615 3000953 SCOP2B (2022-06-29)
L [auth P]SCOP2B SuperfamilySigma2 domain of RNA polymerase sigma factors 8039616 3001393 SCOP2B (2022-06-29)
L [auth P]SCOP2B SuperfamilySigma factor domain-like 8039614 3000953 SCOP2B (2022-06-29)
FSCOP2B SuperfamilySigma factor domain-like 8039615 3000953 SCOP2B (2022-06-29)
FSCOP2B SuperfamilySigma factor domain-like 8039614 3000953 SCOP2B (2022-06-29)
FSCOP2B SuperfamilySigma2 domain of RNA polymerase sigma factors 8039616 3001393 SCOP2B (2022-06-29)
K [auth O]SCOP2B SuperfamilyRPB6/omega subunit-like 8039612 3000189 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRPB6/omega subunit-like 8039612 3000189 SCOP2B (2022-06-29)
J [auth N]SCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8039613 3001330 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8039613 3001330 SCOP2B (2022-06-29)
I [auth M]SCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8039611 3001330 SCOP2B (2022-06-29)
I [auth M]SCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8039611 3001330 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8039611 3001330 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8039611 3001330 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
L [auth P]e3eqlP3 A: HTHX: HTHH: tetra-helical, lambda repressor-likeT: FXa_inhibitionF:ECOD (20:10:01)
L [auth P]e3eqlP4 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: V-setF:ECOD (20:10:01)
Fe3eqlF3 A: HTHX: HTHH: tetra-helical, lambda repressor-likeT: FXa_inhibitionF:ECOD (20:10:01)
Fe3eqlF4 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: V-setF:ECOD (20:10:01)
K [auth O]e3eqlO1 A: HTHX: HTHH: tetra-helical, lambda repressor-likeT: FXa_inhibitionF:ECOD (20:10:01)
Ee3eqlE1 A: HTHX: HTHH: tetra-helical, lambda repressor-likeT: FXa_inhibitionF:ECOD (20:10:01)
J [auth N]e3eqlN1 A: Suppressor of Fused, C-terminal domainX: HTHH: winged helix domainT: GPW_gp25F:ECOD (20:10:01)
J [auth N]e3eqlN34 A: Subtilisin-likeX: Subtilisin-likeH: Subtilisin-likeT: Chorismate_bindF:ECOD (20:10:01)
De3eqlD1 A: beta-GraspX: Ubiquitin-relatedH: Ubiquitin-likeT: MutS_IF:ECOD (20:10:01)
De3eqlD2 A: beta-GraspX: Ubiquitin-relatedH: Ubiquitin-likeT: Big_10F:ECOD (20:10:01)
De3eqlD5 A: RuvA-CX: post-HMGL domain-likeH: post-HMGL domain-likeT: Cobalamin_bindF:ECOD (20:10:01)
I [auth M]e3eqlM3 A: HTHX: HTHH: tetra-helical, lambda repressor-likeT: FXa_inhibitionF:ECOD (20:10:01)
I [auth M]e3eqlM8 A: Four-helical up-and-down bundleX: Thymidylate synthase/dCMP hydroxymethylaseH: Thymidylate synthase/dCMP hydroxymethylaseT: Pectate_lyase_2F:ECOD (20:10:01)
Ce3eqlC3 A: HTHX: HTHH: tetra-helical, lambda repressor-likeT: FXa_inhibitionF:ECOD (20:10:01)
Ce3eqlC8 A: Four-helical up-and-down bundleX: Thymidylate synthase/dCMP hydroxymethylaseH: Thymidylate synthase/dCMP hydroxymethylaseT: Pectate_lyase_2F:ECOD (20:10:01)
H [auth L]e3eqlL1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Exop_CF:ECOD (20:10:01)
G [auth K]e3eqlK1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Exop_CF:ECOD (20:10:01)
Be3eqlB1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Exop_CF:ECOD (20:10:01)
Ae3eqlA1 A: Thioredoxin-likeX: Thioredoxin-likeH: Thioredoxin-likeT: Exop_CF:ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
L [auth P]1.20.120.1810 Mainly Alpha Up-down Bundle Four Helix Bundle (Hemerythrin (Met), subunit A) CATH (4.3.0)
L [auth P]1.10.10.10 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domainCATH (4.3.0)
F1.20.120.1810 Mainly Alpha Up-down Bundle Four Helix Bundle (Hemerythrin (Met), subunit A) CATH (4.3.0)
F1.10.10.10 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domainCATH (4.3.0)
K [auth O]3.90.940.10 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RNA polymerase subunit, RPB6/omegaCATH (4.3.0)
E3.90.940.10 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RNA polymerase subunit, RPB6/omegaCATH (4.3.0)
J [auth N]2.40.50.100 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domainCATH (utative)
J [auth N]2.40.40.20 Mainly Beta Beta Barrel Barwin-like endoglucanases CATH (utative)
J [auth N]1.10.40.90 Mainly Alpha Orthogonal Bundle Ribonucleotide Reductase Protein R1 domain 1CATH (utative)
J [auth N]1.10.274.100 Mainly Alpha Orthogonal Bundle Enzyme I Chain A, domain 2CATH (utative)
J [auth N]1.10.132.30 Mainly Alpha Orthogonal Bundle Topoisomerase I Chain A, domain 4CATH (utative)
J [auth N]3.90.105.10 Alpha Beta Alpha-Beta Complex Molybdopterin biosynthesis moea protein, domain 2 Molybdopterin biosynthesis moea protein, domain 2CATH (utative)
D2.40.50.100 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domainCATH (utative)
D2.40.40.20 Mainly Beta Beta Barrel Barwin-like endoglucanases CATH (utative)
D1.10.40.90 Mainly Alpha Orthogonal Bundle Ribonucleotide Reductase Protein R1 domain 1CATH (utative)
D1.10.274.100 Mainly Alpha Orthogonal Bundle Enzyme I Chain A, domain 2CATH (utative)
D1.10.132.30 Mainly Alpha Orthogonal Bundle Topoisomerase I Chain A, domain 4CATH (utative)
D3.90.105.10 Alpha Beta Alpha-Beta Complex Molybdopterin biosynthesis moea protein, domain 2 Molybdopterin biosynthesis moea protein, domain 2CATH (utative)
I [auth M]2.40.270.10 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: BCATH (4.3.0)
I [auth M]3.90.1100.10 Alpha Beta Alpha-Beta Complex Rna Polymerase Beta Subunit Chain: C,domain 2CATH (4.3.0)
I [auth M]3.90.1110.10 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: BCATH (4.3.0)
I [auth M]2.30.150.10 Mainly Beta Roll Rna Polymerase Beta Subunit Chain: C, domain 4CATH (4.3.0)
I [auth M]2.40.50.100 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domainCATH (4.3.0)
I [auth M]2.40.50.150 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II, Rpb2 subunit, wall domainCATH (4.3.0)
C2.40.270.10 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: BCATH (4.3.0)
C3.90.1100.10 Alpha Beta Alpha-Beta Complex Rna Polymerase Beta Subunit Chain: C,domain 2CATH (4.3.0)
C3.90.1110.10 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: BCATH (4.3.0)
C2.30.150.10 Mainly Beta Roll Rna Polymerase Beta Subunit Chain: C, domain 4CATH (4.3.0)
C2.40.50.100 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domainCATH (4.3.0)
C2.40.50.150 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II, Rpb2 subunit, wall domainCATH (4.3.0)
H [auth L]3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
H [auth L]2.170.120.12 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit Chain A, domain 2CATH (4.3.0)
G [auth K]3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
G [auth K]2.170.120.12 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit Chain A, domain 2CATH (4.3.0)
B3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
B2.170.120.12 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit Chain A, domain 2CATH (4.3.0)
A3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
A2.170.120.12 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit Chain A, domain 2CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
F,
L [auth P]		PF04539Sigma-70 region 3 (Sigma70_r3)Sigma-70 region 3- Family
F,
L [auth P]		PF00140Sigma-70 factor, region 1.2 (Sigma70_r1_2)Sigma-70 factor, region 1.2- Family
F,
L [auth P]		PF04542Sigma-70 region 2 (Sigma70_r2)Sigma-70 region 2Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA ...Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2].
Domain
F,
L [auth P]		PF04545Sigma-70, region 4 (Sigma70_r4)Sigma-70, region 4Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix fami ...Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.
Domain
E,
K [auth O]		PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
D,
J [auth N]		PF00623RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)RNA polymerase Rpb1, domain 2RNA 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,
J [auth N]		PF05000RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)RNA polymerase Rpb1, domain 4RNA 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,
J [auth N]		PF04983RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)RNA polymerase Rpb1, domain 3RNA 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,
J [auth N]		PF04998RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)RNA polymerase Rpb1, domain 5RNA 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,
J [auth N]		PF04997RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)RNA polymerase Rpb1, domain 1RNA 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
C,
I [auth M]		PF04561RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)RNA polymerase Rpb2, domain 2RNA 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
C,
I [auth M]		PF10385RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)RNA polymerase beta subunit external 1 domainRNA 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
C,
I [auth M]		PF04560RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)RNA polymerase Rpb2, domain 7RNA 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
C,
I [auth M]		PF04565RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)RNA polymerase Rpb2, domain 3RNA 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
C,
I [auth M]		PF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
C,
I [auth M]		PF00562RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)RNA polymerase Rpb2, domain 6RNA 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
F,
L [auth P]		RNA polymerase sigma factor rpoD
E,
K [auth O]		DNA-directed RNA polymerase subunit omega
D,
J [auth N]		DNA-directed RNA polymerase subunit beta'
C,
I [auth M]		DNA-directed RNA polymerase subunit beta
A,
B,
G [auth K],
H [auth L]		DNA-directed RNA polymerase subunit alpha

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
F,
L [auth P]		IPR007627RNA polymerase sigma-70 region 2Domain
F,
L [auth P]		IPR000943RNA polymerase sigma-70Domain
F,
L [auth P]		IPR013325RNA polymerase sigma factor, region 2Homologous Superfamily
F,
L [auth P]		IPR013324RNA polymerase sigma factor, region 3/4-likeHomologous Superfamily
F,
L [auth P]		IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
F,
L [auth P]		IPR012760RNA polymerase sigma factor RpoD, C-terminalDomain
F,
L [auth P]		IPR009042RNA polymerase sigma-70 region 1.2Domain
F,
L [auth P]		IPR007630RNA polymerase sigma-70 region 4Domain
F,
L [auth P]		IPR014284RNA polymerase sigma-70-like domainDomain
F,
L [auth P]		IPR007624RNA polymerase sigma-70 region 3Domain
F,
L [auth P]		IPR028630RNA polymerase sigma factor RpoDFamily
F,
L [auth P]		IPR050239Sigma-70 factor family, RNA polymerase initiation factorsFamily
E,
K [auth O]		IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
E,
K [auth O]		IPR003716DNA-directed RNA polymerase, omega subunitFamily
E,
K [auth O]		IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
D,
J [auth N]		IPR007066RNA polymerase Rpb1, domain 3Domain
D,
J [auth N]		IPR007081RNA polymerase Rpb1, domain 5Domain
D,
J [auth N]		IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
D,
J [auth N]		IPR012754DNA-directed RNA polymerase, subunit beta-prime, bacterial typeFamily
D,
J [auth N]		IPR048566DNA-directed RNA polymerase subunit beta', hybrid domainDomain
D,
J [auth N]		IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
D,
J [auth N]		IPR007083RNA polymerase Rpb1, domain 4Domain
D,
J [auth N]		IPR000722RNA polymerase, alpha subunitDomain
D,
J [auth N]		IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
D,
J [auth N]		IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
D,
J [auth N]		IPR006592RNA polymerase, N-terminalDomain
D,
J [auth N]		IPR007080RNA polymerase Rpb1, domain 1Domain
C,
I [auth M]		IPR007642RNA polymerase Rpb2, domain 2Domain
C,
I [auth M]		IPR015712DNA-directed RNA polymerase, subunit 2Family
C,
I [auth M]		IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
C,
I [auth M]		IPR042107DNA-directed RNA polymerase, beta subunit, external 1 domain superfamilyHomologous Superfamily
C,
I [auth M]		IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
C,
I [auth M]		IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
C,
I [auth M]		IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
C,
I [auth M]		IPR007645RNA polymerase Rpb2, domain 3Domain
C,
I [auth M]		IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
C,
I [auth M]		IPR019462DNA-directed RNA polymerase, beta subunit, external 1 domainDomain
C,
I [auth M]		IPR010243DNA-directed RNA polymerase beta subunit, bacterial-typeFamily
C,
I [auth M]		IPR007644RNA polymerase, beta subunit, protrusionDomain
C,
I [auth M]		IPR007641RNA polymerase Rpb2, domain 7Domain
A,
B,
G [auth K],
H [auth L]		IPR011773DNA-directed RNA polymerase, alpha subunitFamily
A,
B,
G [auth K],
H [auth L]		IPR011262DNA-directed RNA polymerase, insert domainDomain
A,
B,
G [auth K],
H [auth L]		IPR011260RNA polymerase, alpha subunit, C-terminalDomain
A,
B,
G [auth K],
H [auth L]		IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
A,
B,
G [auth K],
H [auth L]		IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
A,
B,
G [auth K],
H [auth L]		IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily