1Y1O | pdb_00001y1o

X-ray crystal Structure of Penicillin-binding protein-related factor A from Bacillus stearothermophilus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d1y1od_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	RecU-like	Recombination protein U (RecU)/PBP related factor A (PrfA)	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
C	d1y1oc_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	RecU-like	Recombination protein U (RecU)/PBP related factor A (PrfA)	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d1y1ob_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	RecU-like	Recombination protein U (RecU)/PBP related factor A (PrfA)	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
A	d1y1oa_	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	RecU-like	Recombination protein U (RecU)/PBP related factor A (PrfA)	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Restriction endonuclease-like	8044263	3000104	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Restriction endonuclease-like	8044263	3000104	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Restriction endonuclease-like	8044263	3000104	SCOP2B (2022-06-29)
A	SCOP2 Family	RecU-like	8031885	4003496	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Restriction endonuclease-like	8044263	3000104	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)
D	RecU	e1y1oD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
C	RecU	e1y1oC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
B	RecU	e1y1oB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
A	RecU	e1y1oA1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: RecU	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
C	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
B	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)
A	3.40.1350.10	Alpha Beta	3-Layer(aba) Sandwich	Trna Endonuclease	Chain: A, domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Penicillin-binding protein-related factor A	cation binding magnesium ion binding ion binding binding metal ion binding small molecule 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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule 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 nucleic acid binding	cellular response to stimulus response to stimulus 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 metabolic process cellular process macromolecule metabolic process DNA repair DNA recombination cellular response to stimulus response to stimulus 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 metabolic process cellular process macromolecule metabolic process DNA repair DNA recombination cell cycle chromosome segregation cell cycle process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004612	Holliday junction resolvase RecU	Family
A, B, C, D	IPR011335	Restriction endonuclease type II-like	Homologous Superfamily
A, B, C, D	IPR011856	tRNA endonuclease-like domain 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.