3WOE

Crystal structure of P23-45 gp39 (6-109) bound to Thermus thermophilus RNA polymerase beta-flap domain

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	PF00562	e3woeA1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: PF00562	ECOD (1.6)
C	PF00562	e3woeC1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: PF00562	ECOD (1.6)
B	PF20760	e3woeB1	A: a+b two layers	X: Cystatin-like	H: Thermus phage P23-45 gp39 (From Topology)	T: Thermus phage P23-45 gp39	F: PF20760	ECOD (1.6)
D	PF20760	e3woeD1	A: a+b two layers	X: Cystatin-like	H: Thermus phage P23-45 gp39 (From Topology)	T: Thermus phage P23-45 gp39	F: PF20760	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
C	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
B	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, 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
B, D	PF20760	Thermus phage P23-45 gp39, N-terminal domain (P23-45_gp39_N)	Thermus phage P23-45 gp39, N-terminal domain	This domain is found at the N terminus in the protein gp35 from Thermus phage P23-45 and similar sequences from tailed bacteriophages. This protein binds the host's DNA-dependent RNA polymerase (RNAP), inhibiting host gene transcription while allowin ...	This domain is found at the N terminus in the protein gp35 from Thermus phage P23-45 and similar sequences from tailed bacteriophages. This protein binds the host's DNA-dependent RNA polymerase (RNAP), inhibiting host gene transcription while allowing transcription of phage genes. Structural studies show this core domain of the protein binds to the RNA beta-flap domain. It consists of a central beta sheet and a N-terminal helix [1, 2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	DNA-directed RNA polymerase subunit beta	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance 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
B, D	Putative uncharacterized protein	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR007642	RNA polymerase Rpb2, domain 2	Domain
A, C	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
A, C	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
A, C	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
A, C	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
A, C	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
A, C	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
A, C	IPR007645	RNA polymerase Rpb2, domain 3	Domain
A, C	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
A, C	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
A, C	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
A, C	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
A, C	IPR007641	RNA polymerase Rpb2, domain 7	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.