Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
JSCOP2B SuperfamilyRNA polymerase subunit RPB108042692 3001213 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase8080736 3001655 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRNA polymerase subunits8042695 3001823 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRPB5-like RNA polymerase subunit8035939 3001722 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyEukaryotic RPB5 N-terminal domain8044454 3000444 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRPB6/omega subunit-like8042688 3000189 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like8041967 3002702 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like8093392 3002702 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF00623e5w66A6 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: PF00623ECOD (1.6)
APF00623e5w66A5 A: a+b two layersX: 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-polymeraseF: PF00623ECOD (1.6)
AF_UNCLASSIFIEDe5w66A7 A: a+b two layersX: 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 subunitF: F_UNCLASSIFIEDECOD (1.6)
AF_UNCLASSIFIEDe5w66A2 A: a+b two layersX: 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 subunitF: F_UNCLASSIFIEDECOD (1.6)
APF04997e5w66A1 A: a+b complex topologyX: 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 subunitF: PF04997ECOD (1.6)
APF04998e5w66A4 A: a+b complex topologyX: 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 subunitF: PF04998ECOD (1.6)
AF_UNCLASSIFIEDe5w66A3 A: a+b complex topologyX: helical domain in yeast RNA-polymerasesH: third helical domain in yeast RNA-polymerase I RPA190 subunit (From Topology)T: third helical domain in yeast RNA-polymerase I RPA190 subunitF: F_UNCLASSIFIEDECOD (1.6)
APF04998,PF05000e5w66A9 A: a+b complex topologyX: 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 subunitF: PF04998,PF05000ECOD (1.6)
APF04983e5w66A8 A: a+b complex topologyX: 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 subunitF: PF04983ECOD (1.6)
JPF01194e5w66J1 A: alpha arraysX: HTHH: RPB10 (From Topology)T: RPB10F: PF01194ECOD (1.6)
KPF13656e5w66K1 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: PF13656ECOD (1.6)
LPF03604e5w66L1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF03604ECOD (1.6)
NPF08208e5w66N1 A: beta complex topologyX: triple barrel (From Homology)H: triple barrelT: RNA polymerase I subunits A49/A34.5 dimerization domainsF: PF08208ECOD (1.6)
BPF00562e5w66B4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: PF00562ECOD (1.6)
BPF00562e5w66B1 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: PF00562ECOD (1.6)
BPF04563,PF04565e5w66B7 A: a+b complex topologyX: 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-polymeraseF: PF04563,PF04565ECOD (1.6)
BPF04561e5w66B3 A: a+b complex topologyX: 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-polymeraseF: PF04561ECOD (1.6)
BPF00562e5w66B2 A: a+b complex topologyX: 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-polymeraseF: PF00562ECOD (1.6)
BPF00562,PF04560e5w66B6 A: a+b complex topologyX: 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-polymeraseF: PF00562,PF04560ECOD (1.6)
BPF06883e5w66B5 A: a+b complex topologyX: 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 subunitF: PF06883ECOD (1.6)
CPF01193e5w66C1 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: PF01193ECOD (1.6)
CPF01000e5w66C2 A: a+b complex topologyX: Ribosomal protein TL5/L25 C-terminal domain-likeH: Insert subdomain of RNA polymerase alpha subunit (From Topology)T: Insert subdomain of RNA polymerase alpha subunitF: PF01000ECOD (1.6)
DPF08203e5w66D1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: PF08203ECOD (1.6)
EPF01191e5w66E1 A: a+b two layersX: RPB5-like RNA polymerase subunit (From Topology)H: RPB5-like RNA polymerase subunit (From Topology)T: RPB5-like RNA polymerase subunitF: PF01191ECOD (1.6)
EPF03871e5w66E2 A: a/b three-layered sandwichesX: Restriction endonuclease-likeH: Eukaryotic RPB5 N-terminal domain (From Topology)T: Eukaryotic RPB5 N-terminal domainF: PF03871ECOD (1.6)
FPF01192e5w66F1 A: alpha arraysX: RPB6/omega subunit-like (From Homology)H: RPB6/omega subunit-likeT: RPB6F: PF01192ECOD (1.6)
GPF17875e5w66G1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF17875ECOD (1.6)
GPF03876e5w66G2 A: a+b two layersX: Dodecin subunit-likeH: Flavin-binding protein dodecin-like (From Topology)T: Flavin-binding protein dodecin-likeF: PF03876ECOD (1.6)
HPF03870e5w66H1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF03870ECOD (1.6)
IPF02150e5w66I1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF02150ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
J1.10.10.60 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Homeodomain-likeCATH (4.3.0)
K3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
L2.20.28.30 Mainly Beta Single Sheet Rubrerythrin, domain 2 RNA polymerase ii, chain LCATH (4.3.0)
B3.90.1110.10 Alpha Beta Alpha-Beta Complex Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: BCATH (4.3.0)
B3.90.1070.20 Alpha Beta Alpha-Beta Complex Hypothetical Protein Ta0175 Chain: A, domain 2CATH (4.3.0)
B2.40.270.10 Mainly Beta Beta Barrel Dna-directed Rna Polymerase Ii 140kd Polypeptide Chain: BCATH (4.3.0)
B2.40.50.150 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) RNA polymerase II, Rpb2 subunit, wall domainCATH (4.3.0)
B3.90.1800.10 Alpha Beta Alpha-Beta Complex DCoH-like RNA polymerase alpha subunit dimerisation domainCATH (4.3.0)
C3.30.1360.10 Alpha Beta 2-Layer Sandwich Gyrase A domain 2CATH (4.3.0)
C2.170.120.12 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit Chain A, domain 2CATH (4.3.0)
D6.10.250.3390 Special Helix non-globular Single alpha-helices involved in coiled-coils or other helix-helix interfaces CATH (4.3.0)
E3.40.1340.10 Alpha Beta 3-Layer(aba) Sandwich Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide Chain: ACATH (4.3.0)
E3.90.940.20 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RPB5-like RNA polymerase subunitCATH (4.3.0)
F3.90.940.10 Alpha Beta Alpha-Beta Complex Eukaryotic RPB6 RNA polymerase subunit RNA polymerase subunit, RPB6/omegaCATH (4.3.0)
H2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteinsCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
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
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
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
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
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 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 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
PF01194RNA polymerases N / 8 kDa subunit (RNA_pol_N)RNA polymerases N / 8 kDa subunit- Domain
PF01193RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)RNA polymerase Rpb3/Rpb11 dimerisation domainThe 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
PF13656RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)RNA polymerase Rpb3/Rpb11 dimerisation domainThe 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
PF03604DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD)DNA directed RNA polymerase, 7 kDa subunit- Domain
PF06870A49-like RNA polymerase I associated factor (RNA_pol_I_A49)A49-like RNA polymerase I associated factor- Family
PF08208DNA-directed RNA polymerase I subunit RPA34.5 (RNA_polI_A34)DNA-directed RNA polymerase I subunit RPA34.5- Family
PF20640Rrn6, helical bundle domain (Rrn6_HB)Rrn6, helical bundle domainThis is the helical bundle domain (also referred to as the headlock domain) from RNA polymerase I-specific transcription initiation factor Rrn6, a component of a multisubunit transcription factor essential for the initiation of rDNA transcription by ...This is the helical bundle domain (also referred to as the headlock domain) from RNA polymerase I-specific transcription initiation factor Rrn6, a component of a multisubunit transcription factor essential for the initiation of rDNA transcription by Pol I [1,2]. This is a helical domain found towards the C-terminal, adjacent the beta-propeller, that wraps around Rrn7 and is part of module II of the core factor (CF) [2]. The DNA-bound CF resembles a right hand in which the N-terminal regions of both Rrn11 and Rrn6 (the beta-propeller domain) constitutes the palm, the thumb is composed of the C-terminal of Rrn11 and the fingers and knuckles correspond to Rrn7 and the C-terminal half of Rrn6 (this domain), respectively [3].
Domain
PF20639RRN6, K-rich C-terminal domain (Rrn6_K-rich)RRN6, K-rich C-terminal domainThis is the C-terminal K-rich domain from RNA polymerase I-specific transcription initiation factor Rrn6 [1]. Rrn6 is a component of a multisubunit transcription factor essential for the initiation of rDNA transcription by Pol I [1,2].Domain
PF10214Rrn6, beta-propeller (Rrn6_beta-prop)Rrn6, beta-propeller- Repeat
PF20644Rrn7/TAF1B, N-terminal cyclin domain (Rrn7_cyclin_N)Rrn7/TAF1B, N-terminal cyclin domainRrn7 from yeast and its orthologue TATA box-binding protein-associated factor RNA polymerase I subunit B (TAF1B) from human, are TFIIB-like factors components of RNA polymerase I core factor complex. They contain two cyclin fold domains which interac ...Rrn7 from yeast and its orthologue TATA box-binding protein-associated factor RNA polymerase I subunit B (TAF1B) from human, are TFIIB-like factors components of RNA polymerase I core factor complex. They contain two cyclin fold domains which interact with both Rrn6 and Rrn11 and form the fingers of the core factor which resembles a right hand. N-terminal regions of both Rrn11 and Rrn6 compose the palm, the thumb is composed by the C-terminal of Rrn11 and the knuckles consist of the C-terminal half of Rrn6. This is the first cyclin domain (cyclin I) from yeast Rrn7 and its orthologues from animals and plants TAF1B [1,2].
Domain
PF20645Rrn7/TAF1B, C-terminal cyclin domain (Rrn7_cyclin_C)Rrn7/TAF1B, C-terminal cyclin domainRrn7 from yeast and its orthologue TATA box-binding protein-associated factor RNA polymerase I subunit B (TAF1B) from human, are TFIIB-like factors components of RNA polymerase I core factor complex. They contain two cyclin fold domains. In Rrn7 the ...Rrn7 from yeast and its orthologue TATA box-binding protein-associated factor RNA polymerase I subunit B (TAF1B) from human, are TFIIB-like factors components of RNA polymerase I core factor complex. They contain two cyclin fold domains. In Rrn7 the cyclin domains interact with both Rrn6 and Rrn11 and form the fingers of the core factor which resembles a right hand. N-terminal regions of both Rrn11 and Rrn6 compose the palm, the thumb is composed by the C-terminal of Rrn11 and the knuckles consist of the C-terminal half of Rrn6. This is the C-terminal cyclin domain of Rrn7 from yeast and the orthologues from animals and plants TAF1B [1,2].
Domain
PF04090RNA polymerase I-specific transcription initiation factor Rrn11 (Rrn11)RNA polymerase I-specific transcription initiation factor Rrn11- Repeat
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
PF06883RNA polymerase I, Rpa2 specific domain (RNA_pol_Rpa2_4)RNA polymerase I, Rpa2 specific domainThis domain is found between domain 3 (Pfam:PF04565) and domain 5 (Pfam:PF04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate mo ...This domain is found between domain 3 (Pfam:PF04565) and domain 5 (Pfam:PF04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability [1].
Domain
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
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
PF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
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
PF01193RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)RNA polymerase Rpb3/Rpb11 dimerisation domainThe 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
PF01000RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)RNA polymerase Rpb3/RpoA insert domainMembers of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaealDomain
PF08203Yeast RNA polymerase I subunit RPA14 (RNA_polI_A14)Yeast RNA polymerase I subunit RPA14- Family
PF01191RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)RNA polymerase Rpb5, C-terminal domainThe assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.Domain
PF03871RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N)RNA polymerase Rpb5, N-terminal domainRpb5 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
PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
PF17875RPA43 OB domain in RNA Pol I (RPA43_OB)RPA43 OB domain in RNA Pol IThis is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rp ...This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rpb4/7 in Pol II and C17/25 in Pol III [1]. Crystal structure analysis show that A43-A14 heterodimer forms the stalk that provides a platform for initiation factors and interacts with newly synthesized RNA [3].
Domain
PF03876SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].
Domain
PF03870RNA polymerase Rpb8 (RNA_pol_Rpb8)RNA polymerase Rpb8- Family
PF02150RNA polymerases M/15 Kd subunit (RNA_POL_M_15KD)RNA polymerases M/15 Kd subunit- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
DNA-directed RNA polymerase I subunit RPA190
DNA-directed RNA polymerases I, II, and III subunit RPABC5
DNA-directed RNA polymerases I and III subunit RPAC2
DNA-directed RNA polymerases I, II, and III subunit RPABC4
DNA-directed RNA polymerase I subunit RPA49
DNA-directed RNA polymerase I subunit RPA34
RNA polymerase I-specific transcription initiation factor RRN6
RNA polymerase I-specific transcription initiation factor RRN7
RNA polymerase I-specific transcription initiation factor RRN11
RNA---
non-template strand DNA---
DNA-directed RNA polymerase I subunit RPA135
template strand DNA---
DNA-directed RNA polymerases I and III subunit RPAC1
DNA-directed RNA polymerase I subunit RPA14
DNA-directed RNA polymerases I, II, and III subunit RPABC1
DNA-directed RNA polymerases I, II, and III subunit RPABC2
DNA-directed RNA polymerase I subunit RPA43
DNA-directed RNA polymerases I, II, and III subunit RPABC3
DNA-directed RNA polymerase I subunit RPA12

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR007081RNA polymerase Rpb1, domain 5Domain
IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
IPR047107DNA-directed RNA pol I, largest subunit, C-terminal domainDomain
IPR007083RNA polymerase Rpb1, domain 4Domain
IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
IPR006592RNA polymerase, N-terminalDomain
IPR007066RNA polymerase Rpb1, domain 3Domain
IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
IPR000722RNA polymerase, alpha subunitDomain
IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
IPR015699DNA-directed RNA pol I, largest subunit, N-terminal domainDomain
IPR007080RNA polymerase Rpb1, domain 1Domain
IPR020789RNA polymerases, subunit N, zinc binding siteBinding Site
IPR000268DNA-directed RNA polymerase subunit RPABC5/Rpb10Family
IPR023580RNA polymerase subunit RPB10Homologous Superfamily
IPR009025DNA-directed RNA polymerase, RBP11-like dimerisation domainDomain
IPR022905DNA-directed RNA polymerase subunit Rpo11-likeFamily
IPR033898DNA-directed RNA polymerases I and III subunit AC19Family
IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
IPR008193DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved siteConserved Site
IPR006591RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4Family
IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4Homologous Superfamily
IPR039747DNA-directed RNA polymerases I, II, and III subunit RPABC4Family
IPR009668RNA polymerase I associated factor, A49-likeFamily
IPR013240DNA-directed RNA polymerase I, subunit RPA34Family
IPR048535RRN6, beta-propellerDomain
IPR016531RNA polymerase I-specific transcription initiation factor Rrn6Family
IPR048536RRN6, K-rich C-terminal domainDomain
IPR048537RRN6, helical bundle domainDomain
IPR019350RNA polymerase I-specific transcription initiation factor RRN6-likeFamily
IPR033599RNA polymerase I transcription initiation factor TAF1B/Rrn7Family
IPR048540Rrn7/TAF1B, N-terminal cyclin domainDomain
IPR048538Rrn7/TAF1B, C-terminal cyclin domainDomain
IPR021752Transcription initiation factor Rrn7, Zinc-fingerDomain
IPR007224Transcription initiation factor Rrn11Family
IPR016850Transcription initiation factor Rrn11, budding yeastFamily
IPR007642RNA polymerase Rpb2, domain 2Domain
IPR015712DNA-directed RNA polymerase, subunit 2Family
IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
IPR009674DNA-directed RNA polymerase I subunit RPA2, domain 4Domain
IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
IPR007645RNA polymerase Rpb2, domain 3Domain
IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
IPR007644RNA polymerase, beta subunit, protrusionDomain
IPR007641RNA polymerase Rpb2, domain 7Domain
IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
IPR022842DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1Family
IPR033901DNA-directed RNA polymerases I and III subunit AC40Family
IPR001514DNA-directed RNA polymerase, 30-40kDa subunit, conserved siteConserved Site
IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
IPR011262DNA-directed RNA polymerase, insert domainDomain
IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
IPR013239RNA polymerase I, subunit Rpa14, fungiFamily
IPR036710RNA polymerase Rpb5, N-terminal domain superfamilyHomologous Superfamily
IPR014381DNA-directed RNA polymerase subunit Rpo5/Rpb5Family
IPR035913RPB5-like RNA polymerase subunit superfamilyHomologous Superfamily
IPR000783RNA polymerase, subunit H/Rpb5 C-terminalDomain
IPR020608RNA polymerase, subunit H/Rpb5, conserved siteConserved Site
IPR005571RNA polymerase, Rpb5, N-terminalDomain
IPR028363DNA-directed RNA polymerase, subunit RPB6Family
IPR006111Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunitFamily
IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved siteConserved Site
IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
IPR045113RNA polymerase subunit Rpb7-likeFamily
IPR005576RNA polymerase Rpb7-like , N-terminalDomain
IPR036898RNA polymerase Rpb7-like, N-terminal domain superfamilyHomologous Superfamily
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR041178RPA43, OB domainDomain
IPR041901Rpa43, N-terminal ribonucleoprotein (RNP) domainDomain
IPR005570DNA-directed RNA polymerases I, II, and III subunit RPABC3Family
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR034004Pol I subunit A12, C-terminal zinc ribbonDomain
IPR012164DNA-directed RNA polymerase subunit/transcription factor SFamily
IPR001222Zinc finger, TFIIS-typeDomain
IPR019761DNA-directed RNA polymerase M, 15kDa subunit, conserved siteConserved Site
IPR001529DNA-directed RNA polymerase, M/15kDa subunitDomain