Annotations: 8B1R

RecBCD in complex with the phage protein gp5.9

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth D]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043248	3002019	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043246	3002019	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Restriction endonuclease-like	8043247	3000104	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043245	3002019	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043241	3002019	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8043242	3002019	SCOP2B (2022-06-29)
A [auth B]	SCOP2B Superfamily	Restriction endonuclease-like	8043244	3000104	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth Q]	SecE	e8b1rQ1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: SecE	ECOD (v294.2)
D [auth P]	SecE	e8b1rP1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: SecE	ECOD (v294.2)
C [auth D]	RecD_N	e8b1rD1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: RecD_N	ECOD (v294.2)
B [auth C]	RecD_N	e8b1rC1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: RecD_N	ECOD (v294.2)
A [auth B]	RecD_N	e8b1rB1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: RecD_N	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	1.10.10.1020	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	RecBCD complex, subunit RecD, N-terminal domain	CATH (utative)
C [auth D]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth P], E [auth Q]	PF25708	Phage T7 gp5.9 RecBCD inhibitor (Phage_T7_Gp5_9)	Phage T7 gp5.9 RecBCD inhibitor	-	Family
C [auth D]	PF21185	RecBCD enzyme subunit RecD, N-terminal domain (RecD_N)	RecBCD enzyme subunit RecD, N-terminal domain	This domain is found in RecBCD enzyme subunit RecD from Escherichia coli and in similar proteins mostly found in Gammaproteobacteria. RecD is a 5'-3' helicase that comprises three domains. This entry represents the N-terminal domain of RecD, which fo ...	This domain is found in RecBCD enzyme subunit RecD from Escherichia coli and in similar proteins mostly found in Gammaproteobacteria. RecD is a 5'-3' helicase that comprises three domains. This entry represents the N-terminal domain of RecD, which forms the principal interface between RecD and domain 2B of RecC and leads to the conformational change in RecD that has significant effects on the conformation of the RecC subunit [1-4].	Domain
C [auth D]	PF13245	AAA domain (AAA_19)	AAA domain		Domain
B [auth C]	PF04257	RecC, N-terminal domain (RecC_N)	RecC, N-terminal domain	The Exodeoxyribonuclease V enzyme is a multi-subunit enzyme comprised of the proteins RecB, RecC (this family) and RecD. This enzyme plays an important role in homologous genetic recombination, repair of double strand DNA breaks resistance to UV irra ...	The Exodeoxyribonuclease V enzyme is a multi-subunit enzyme comprised of the proteins RecB, RecC (this family) and RecD. This enzyme plays an important role in homologous genetic recombination, repair of double strand DNA breaks resistance to UV irradiation and chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyses ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of ssDNA or dsDNA and unwinding of dsDNA [1]. This subunit recognises and binds DNA forks containing Chi sequences in a sequence specific manner while Chi interactions with the phosphodiester backbone (mainly arginine side chains) stabilise the twisted conformation of the DNA. These interactions induce conformational changes that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition, to constructive host DNA repair [2]. This entry represents the N-terminal domain.	Domain
B [auth C]	PF17946	RecC C-terminal domain (RecC_C)	RecC C-terminal domain	This entry corresponds to the C-terminal domain of the RecC protein. This domain has a PD(D/E)XK like fold. Deleting this domain eliminates RecD assembly within the RecBCD complex [1].	Domain
A [auth B]	PF13361	UvrD-like helicase C-terminal domain (UvrD_C)	UvrD-like helicase C-terminal domain	This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold.	Domain
A [auth B]	PF00580	UvrD/REP helicase N-terminal domain (UvrD-helicase)	UvrD/REP helicase N-terminal domain	The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near t ...	The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family.	Domain
A [auth B]	PF12705	PD-(D/E)XK nuclease superfamily (PDDEXK_1)	PD-(D/E)XK nuclease superfamily	Members of this family belong to the PD-(D/E)XK nuclease superfamily	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth P], E [auth Q]	Probable RecBCD inhibitor gp5.9	-	symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction	-
C [auth D]	RecBCD enzyme subunit RecD	nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity binding adenyl ribonucleotide binding nucleotide binding nucleic acid conformation isomerase activity isomerase activity DNA helicase activity catalytic activity, acting on a nucleic acid helicase activity ATP-dependent activity ATP-dependent activity, acting on DNA catalytic activity, acting on DNA 5'-3' DNA helicase activity catalytic activity macromolecular conformation isomerase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding DNA exonuclease activity hydrolase activity exodeoxyribonuclease V activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity nuclease activity hydrolase activity, acting on ester bonds exonuclease activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides single-stranded DNA helicase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of DNA recombination regulation of cellular process regulation of double-strand break repair regulation of cellular response to stress negative regulation of biological process regulation of primary metabolic process negative regulation of DNA repair nucleobase-containing compound metabolic process regulation of response to stress negative regulation of double-strand break repair negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process recombinational repair regulation of nucleobase-containing compound metabolic process negative regulation of double-strand break repair via homologous recombination double-strand break repair via homologous recombination DNA repair negative regulation of macromolecule metabolic process double-strand break repair regulation of biological process negative regulation of response to stimulus negative regulation of metabolic process DNA recombination biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair regulation of double-strand break repair via homologous recombination negative regulation of DNA recombination regulation of response to stimulus metabolic process negative regulation of DNA metabolic process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA double-strand break processing regulation of DNA double-strand break processing DNA-templated DNA replication DNA replication	protein-containing complex catalytic complex exodeoxyribonuclease V complex intracellular protein-containing complex
B [auth C]	RecBCD enzyme subunit RecC	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding DNA exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exodeoxyribonuclease V activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity ATP-dependent activity, acting on DNA nucleic acid conformation isomerase activity isomerase activity DNA helicase activity helicase activity macromolecular conformation isomerase activity ATP-dependent activity	cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process cellular process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair response to radiation response to abiotic stimulus biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids response to biotic stimulus defense response to other organism response to external biotic stimulus	protein-containing complex catalytic complex exodeoxyribonuclease V complex intracellular protein-containing complex
A [auth B]	RecBCD enzyme subunit RecB	DNA exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exodeoxyribonuclease V activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity DNA endonuclease activity endonuclease activity ATP-dependent activity, acting on DNA DNA exonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exodeoxyribonuclease V activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity exonuclease activity DNA endonuclease activity endonuclease activity ATP-dependent activity, acting on DNA ATP-dependent activity nucleic acid conformation isomerase activity isomerase activity DNA helicase activity helicase activity macromolecular conformation isomerase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding DNA binding nucleic acid binding DNA translocase activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides 3'-5' DNA helicase activity	response to stimulus response to radiation response to abiotic stimulus nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair cellular response to stress response to stimulus response to radiation response to abiotic stimulus nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids response to biotic stimulus defense response to other organism response to external biotic stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex exodeoxyribonuclease V complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth P], E [auth Q]	IPR058007	Gp5.9	Family
C [auth D]	IPR006344	RecBCD enzyme subunit RecD	Family
C [auth D]	IPR050534	Replicase polyprotein 1ab-like	Family
C [auth D]	IPR049550	RecBCD enzyme subunit RecD, N-terminal domain	Domain
C [auth D]	IPR003593	AAA+ ATPase domain	Domain
C [auth D]	IPR027785	UvrD-like helicase C-terminal domain	Domain
C [auth D]	IPR041851	RecBCD enzyme subunit RecD, N-terminal domain superfamily	Homologous Superfamily
C [auth D]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B [auth C]	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
B [auth C]	IPR041500	RecBCD enzyme subunit RecC, C-terminal	Domain
B [auth C]	IPR006697	RecBCD enzyme subunit RecC	Family
B [auth C]	IPR013986	DExx box DNA helicase domain superfamily	Homologous Superfamily
B [auth C]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth B]	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A [auth B]	IPR014017	UvrD-like helicase, C-terminal	Domain
A [auth B]	IPR004586	RecBCD enzyme subunit RecB	Family
A [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth B]	IPR038726	PD-(D/E)XK endonuclease-like domain, AddAB-type	Domain
A [auth B]	IPR000212	UvrD-like helicase	Family
A [auth B]	IPR011604	PD-(D/E)XK endonuclease-like domain superfamily	Homologous Superfamily
A [auth B]	IPR014016	UvrD-like helicase, ATP-binding domain	Domain