1HJR | pdb_00001hjr

ATOMIC STRUCTURE OF THE RUVC RESOLVASE: A HOLLIDAY JUNCTION-SPECIFIC ENDONUCLEASE FROM E. COLI

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)
A	d1hjra_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	RuvC resolvase	RuvC resolvase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1hjrb_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	RuvC resolvase	RuvC resolvase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1hjrc_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	RuvC resolvase	RuvC resolvase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1hjrd_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	RuvC resolvase	RuvC resolvase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	RuvC resolvase	8032170	4000553	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease H-like	8044548	3000143	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8044548	3000143	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease H-like	8044548	3000143	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8044548	3000143	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)
A	RuvC	e1hjrA1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RuvC	ECOD (1.6)
B	RuvC	e1hjrB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RuvC	ECOD (1.6)
C	RuvC	e1hjrC1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RuvC	ECOD (1.6)
D	RuvC	e1hjrD1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RuvC	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
D	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02075	Crossover junction endodeoxyribonuclease RuvC (RuvC)	Crossover junction endodeoxyribonuclease RuvC	This entry includes endodeoxyribonucleases found in bacteria, such as RuvC. RuvC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli RuvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-she ...	This entry includes endodeoxyribonucleases found in bacteria, such as RuvC. RuvC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli RuvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices [2]. The Escherichia coli RuvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination [1]. RuvC protein (EC:3.1.22.4) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	HOLLIDAY JUNCTION RESOLVASE (RUVC)	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity crossover junction DNA endonuclease activity DNA nuclease activity DNA endonuclease activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity crossover junction DNA endonuclease activity DNA nuclease activity DNA endonuclease activity DNA endonuclease activity, producing 3'-phosphomonoesters catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity	cellular response to stimulus 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 cellular response to stimulus 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 DNA repair DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity replication fork reversal DNA replication replication fork processing response to radiation response to abiotic stimulus	protein-containing complex catalytic complex endodeoxyribonuclease complex Holliday junction resolvase complex intracellular protein-containing complex endonuclease complex cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D	IPR020563	Crossover junction endodeoxyribonuclease RuvC, magnesium-binding site	Binding Site
A, B, C, D	IPR002176	Crossover junction endodeoxyribonuclease RuvC	Family
A, B, C, D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

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.