1YD0

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Thermotoga maritima bound to its catalytic divalent cation: manganese

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	GIY-YIG_1	e1yd0A1	A: a+b three layers	X: GIY-YIG endonuclease (From Topology)	H: GIY-YIG endonuclease (From Topology)	T: GIY-YIG endonuclease	F: GIY-YIG_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1440.10	Alpha Beta	3-Layer(aba) Sandwich	GIY-YIG endonuclease	GIY-YIG endonuclease	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01541	GIY-YIG catalytic domain (GIY-YIG)	GIY-YIG catalytic domain	This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and ...	This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices [4]. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	UvrABC system protein C	excinuclease ABC activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity DNA binding binding organic cyclic compound binding nucleic acid binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process heterocycle metabolic process nucleotide-excision repair nitrogen compound metabolic process metabolic process macromolecule metabolic process cellular aromatic compound metabolic process DNA repair response to extracellular stimulus SOS response response to external stimulus cell communication cellular response to extracellular stimulus cellular response to external stimulus	protein-containing complex catalytic complex excinuclease repair complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex DNA repair complex intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004791	UvrABC system, subunit C	Family
A	IPR036876	UVR domain superfamily	Homologous Superfamily
A	IPR001162	UvrC, RNAse H endonuclease domain	Domain
A	IPR010994	RuvA domain 2-like	Homologous Superfamily
A	IPR038476	UvrC, RNAse H endonuclease domain superfamily	Homologous Superfamily
A	IPR001943	UVR domain	Domain
A	IPR047296	UvrC/Cho-like, GIY-YIG domain	Domain
A	IPR035901	GIY-YIG endonuclease superfamily	Homologous Superfamily
A	IPR000305	GIY-YIG endonuclease	Domain

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.