1KCF | pdb_00001kcf

Crystal Structure of the Yeast Mitochondrial Holliday Junction Resolvase, Ydc2

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)
B	d1kcfb1	All alpha proteins	LEM/SAP HeH motif	SAP domain	SAP domain	Mitochondrial resolvase ydc2 N-terminal domain	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
B	d1kcfb2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Mitochondrial resolvase ydc2 catalytic domain	Mitochondrial resolvase ydc2 catalytic domain	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
A	d1kcfa1	All alpha proteins	LEM/SAP HeH motif	SAP domain	SAP domain	Mitochondrial resolvase ydc2 N-terminal domain	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)
A	d1kcfa2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Mitochondrial resolvase ydc2 catalytic domain	Mitochondrial resolvase ydc2 catalytic domain	fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ribonuclease H-like	8038034	3000143	SCOP2B (2022-06-29)
A	SCOP2 Family	SAP domain	8025652	4002795	SCOP2 (2022-06-29)
A	SCOP2 Family	Mitochondrial resolvase ydc2 catalytic domain	8025655	4003295	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SAP domain	8038031	3001760	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribonuclease H-like	8038034	3000143	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e1kcfB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: p53 tetramerization domain	H: p53 tetramerization domain	T: EF-hand_1,S_100	F:	ECOD (20:10:01)
B		e1kcfB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Hexokinase_2	F:	ECOD (20:10:01)
A		e1kcfA1	A: LEM/SAP HeH motif-like	X: LEM/SAP HeH motif	H: LEM/SAP HeH motif	T: SAP	F:	ECOD (20:10:01)
A		e1kcfA2	A: Ribonuclease H-like	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ydc2-catalyt	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	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	PF09159	Mitochondrial resolvase Ydc2 / RNA splicing MRS1 (Ydc2-catalyt)	Mitochondrial resolvase Ydc2 / RNA splicing MRS1	Members of this family adopt a secondary structure consisting of two beta sheets and one alpha helix, arranged as a beta-alpha-beta motif. Each beta sheet has five strands, arranged in a 32145 order, with the second strand being antiparallel to the ...	Members of this family adopt a secondary structure consisting of two beta sheets and one alpha helix, arranged as a beta-alpha-beta motif. Each beta sheet has five strands, arranged in a 32145 order, with the second strand being antiparallel to the rest. Mitochondrial resolvase Ydc2 is capable of resolving Holliday junctions and cleaves DNA after 5'-CT-3' and 5'-TT-3' sequences [1]. This family also contains the mitochondrial RNA-splicing protein MRS1 which is involved in the excision of group I introns [2-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	HYPOTHETICAL 30.2 KD PROTEIN C25G10.02 IN CHROMOSOME I	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 hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity DNA secondary structure binding DNA binding crossed form four-way junction DNA 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 hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity DNA secondary structure binding DNA binding crossed form four-way junction DNA binding binding four-way junction DNA binding nucleic acid binding flap-structured DNA binding Y-form DNA binding cation binding ion binding metal ion binding small molecule binding	nucleobase-containing compound metabolic process metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process mitochondrial DNA metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B	IPR003034	SAP domain	Domain
A, B	IPR036361	SAP domain superfamily	Homologous Superfamily
A, B	IPR039197	Mrs1/Cce1	Family
A, B	IPR015242	Mitochondrial resolvase Ydc2, catalytic	Domain
A, B	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.