2QNC

Crystal structure of T4 Endonuclease VII N62D mutant in complex with a DNA Holliday junction

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E [auth A]	d2qnca1	All alpha proteins	LEM/SAP HeH motif	Recombination endonuclease VII, C-terminal and dimerization domains	Recombination endonuclease VII, C-terminal and dimerization domains	Recombination endonuclease VII, C-terminal and dimerization domains	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
E [auth A]	d2qnca2	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	Recombination endonuclease VII, N-terminal domain	Recombination endonuclease VII, N-terminal domain	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
F [auth B]	d2qncb1	All alpha proteins	LEM/SAP HeH motif	Recombination endonuclease VII, C-terminal and dimerization domains	Recombination endonuclease VII, C-terminal and dimerization domains	Recombination endonuclease VII, C-terminal and dimerization domains	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
F [auth B]	d2qncb2	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	Recombination endonuclease VII, N-terminal domain	Recombination endonuclease VII, N-terminal domain	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E [auth A]	SCOP2B Superfamily	Recombination endonuclease VII C-terminal and dimerization domains	8035467	3001784	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	His-Me finger endonucleases	8035472	3001893	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	Recombination endonuclease VII C-terminal and dimerization domains	8035467	3001784	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	His-Me finger endonucleases	8035472	3001893	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 A]	Endonuc-dimeris	e2qncA1	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Endonuc-dimeris	ECOD (1.6)
E [auth A]	Endonuclease_7	e2qncA2	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_7	ECOD (1.6)
F [auth B]	Endonuc-dimeris	e2qncB1	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Endonuc-dimeris	ECOD (1.6)
F [auth B]	Endonuclease_7	e2qncB2	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Endonuclease_7	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E [auth A]	3.40.1800.10	Alpha Beta	3-Layer(aba) Sandwich	His-Me finger endonuclease fold	His-Me finger endonucleases	CATH (4.3.0)
E [auth A]	1.10.720.10	Mainly Alpha	Orthogonal Bundle	Transcription Termination Factor Rho, Rna-binding Domain	Chain A, Domain 1	CATH (4.3.0)
F [auth B]	3.40.1800.10	Alpha Beta	3-Layer(aba) Sandwich	His-Me finger endonuclease fold	His-Me finger endonucleases	CATH (4.3.0)
F [auth B]	1.10.720.10	Mainly Alpha	Orthogonal Bundle	Transcription Termination Factor Rho, Rna-binding Domain	Chain A, Domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B]	PF09124	T4 recombination endonuclease VII, dimerisation (Endonuc-dimeris)	T4 recombination endonuclease VII, dimerisation	Members of this family, which are predominantly found in Bacteriophage T4 recombination endonuclease VII, adopt a helical secondary structure, with three alpha helices oriented parallel to each other. They mediate dimerisation of the protein, as well ...	Members of this family, which are predominantly found in Bacteriophage T4 recombination endonuclease VII, adopt a helical secondary structure, with three alpha helices oriented parallel to each other. They mediate dimerisation of the protein, as well as binding to the DNA major groove [1].	Domain
E [auth A], F [auth B]	PF02945	Recombination endonuclease VII (Endonuclease_7)	Recombination endonuclease VII	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	DNA (5'-D(DCPDGDAPDAPDGPDAPDAPDTPDTPDCPDCPDGPDGPDAPDTPDTPDAPDGPDGPDGPDAPDTPDCPDC)-3')	-	-	-
B [auth D]	DNA (5'-D(DGPDGPDAPDTPDCPDCPDCPDTPDAPDAPDGPDCPDTPDCPDCPDAPDTPDCPDGPDAPDTPDGPDTPDG)-3')	-	-	-
C [auth E]	DNA (5'-D(DCPDAPDCPDAPDTPDCPDGPDAPDTPDGPDGPDAPDGPDCPDCPDGPDCPDTPDAPDGPDGPDCPDCPDT)-3')	-	-	-
D [auth F]	DNA (5'-D(DAPDGPDGPDCPDCPDTPDAPDGPDCPDGPDTPDCPDCPDGPDGPDAPDAPDTPDTPDCPDTPDTPDCPDG)-3')	-	-	-
E [auth A], F [auth B]	Recombination endonuclease VII	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B]	IPR004211	Recombination endonuclease VII	Family
E [auth A], F [auth B]	IPR038563	Recombination endonuclease VII superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR036309	T4 recombination endonuclease VII, dimerisation domain superfamily	Homologous Superfamily
E [auth A], F [auth B]	IPR015208	T4 recombination endonuclease VII, dimerisation	Domain
E [auth A], F [auth B]	IPR044925	His-Me finger superfamily	Homologous Superfamily

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.