8I24 | pdb_00008i24

Clostridium thermocellum RNA polymerase transcription open complex with SigI6 and its promoter

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Amino_oxidase	e8i24F01	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Amino_oxidase	ECOD (v294.1)
E	Cullin_AB	e8i24E1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
D	Cullin_AB	e8i24D1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
B [auth A]	Cullin_AB	e8i24A1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)
A [auth B]	Cullin_AB	e8i24B1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Cullin_AB	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
D	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
D	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
D	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
D	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
C	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
C	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
C	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
C	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
C	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
C	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
A [auth B], B [auth A]	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
A [auth B], B [auth A]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H [auth P]	DNA (80-mer)	-	-	-
G [auth O]	DNA (80-mer)	-	-	-
F	RNA polymerase sigma factor SigI6	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
E	DNA-directed RNA polymerase subunit omega	DNA binding binding nucleic acid binding DNA-directed 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	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule 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
D	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 DNA-directed 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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding DNA-directed 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 transition metal ion binding zinc ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule 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
C	DNA-directed RNA polymerase subunit beta	DNA binding binding nucleic acid binding DNA-directed 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 ribonucleoside binding nucleoside binding DNA binding binding nucleic acid binding DNA-directed 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 ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule 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
A [auth B], B [auth A]	DNA-directed RNA polymerase subunit alpha	DNA binding binding nucleic acid binding protein binding protein dimerization activity DNA-directed 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	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
F	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
F	IPR014244	RNA polymerase sigma-I type	Family
E	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
E	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
E	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
D	IPR007066	RNA polymerase Rpb1, domain 3	Domain
D	IPR007081	RNA polymerase Rpb1, domain 5	Domain
D	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
D	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
D	IPR007083	RNA polymerase Rpb1, domain 4	Domain
D	IPR000722	RNA polymerase, alpha subunit	Domain
D	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
D	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
D	IPR006592	RNA polymerase, N-terminal	Domain
D	IPR007080	RNA polymerase Rpb1, domain 1	Domain
C	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
C	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
C	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
C	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
C	IPR007641	RNA polymerase Rpb2, domain 7	Domain
A [auth B], B [auth A]	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
A [auth B], B [auth A]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A [auth B], B [auth A]	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
A [auth B], B [auth A]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A [auth B], B [auth A]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
A [auth B], B [auth A]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily