3WOF | pdb_00003wof

Crystal structure of P23-45 gp39 (6-132) 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)
X	P23-45_gp39_N	e3wofX1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
V	P23-45_gp39_N	e3wofV1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
T	P23-45_gp39_N	e3wofT1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
R	P23-45_gp39_N	e3wofR1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
P	P23-45_gp39_N	e3wofP1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
N	P23-45_gp39_N	e3wofN1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
L	P23-45_gp39_N	e3wofL1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
J	P23-45_gp39_N	e3wofJ1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
H	P23-45_gp39_N	e3wofH1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
F	P23-45_gp39_N	e3wofF1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
D	P23-45_gp39_N	e3wofD1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
B	P23-45_gp39_N	e3wofB1	A: alpha arrays	X: Glycosyl hydrolase domain-like	H: alpha/alpha toroid	T: alpha/alpha toroid	F: P23-45_gp39_N	ECOD (v295.2)
W	Thymidylat_synt	e3wofW1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
U	Thymidylat_synt	e3wofU1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
S	Thymidylat_synt	e3wofS1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
Q	Thymidylat_synt	e3wofQ1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
O	Thymidylat_synt	e3wofO1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
M	Thymidylat_synt	e3wofM1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
K	Thymidylat_synt	e3wofK1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
I	Thymidylat_synt	e3wofI1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
G	Thymidylat_synt	e3wofG1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
E	Thymidylat_synt	e3wofE1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
C	Thymidylat_synt	e3wofC1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)
A	Thymidylat_synt	e3wofA1	A: alpha arrays	X: Four-helical up-and-down bundle	H: Thymidylate synthase/dCMP hydroxymethylase	T: Thymidylate synthase/dCMP hydroxymethylase	F: Thymidylat_synt	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
X	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
V	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
T	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
R	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
P	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
N	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
L	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
J	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
H	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
F	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)
B	2.30.30.1250	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
W	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
U	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
S	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
Q	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
O	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
M	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
K	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
I	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
G	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.3.0)
E	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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	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
B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	Putative uncharacterized protein	-	-	-
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L, N, P, R, T, V, X	IPR057276	Thermus phage P23-45 gp39, N-terminal	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR007642	RNA polymerase Rpb2, domain 2	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR007645	RNA polymerase Rpb2, domain 3	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	IPR007641	RNA polymerase Rpb2, domain 7	Domain

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.