1YD6 | pdb_00001yd6

Crystal structure of the GIY-YIG N-terminal endonuclease domain of UvrC from Bacillus caldotenax

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)
D	Sigma_1_2	e1yd6D1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (develop294)
C	Sigma_1_2	e1yd6C1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (develop294)
B	Sigma_1_2	e1yd6B1	A: alpha bundles	X: HTH	H: Nudix	T: winged helix domain	F: Sigma_1_2	ECOD (develop294)
A	Glucosamine_iso	e1yd6A1	A: alpha bundles	X: Globin-like	H: Ring-building motif I in type III secretion system	T: Ring-building motif I in type III secretion system	F: Glucosamine_iso	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.1440.10	Alpha Beta	3-Layer(aba) Sandwich	GIY-YIG endonuclease	GIY-YIG endonuclease	CATH (4.3.0)
C	3.40.1440.10	Alpha Beta	3-Layer(aba) Sandwich	GIY-YIG endonuclease	GIY-YIG endonuclease	CATH (4.3.0)
B	3.40.1440.10	Alpha Beta	3-Layer(aba) Sandwich	GIY-YIG endonuclease	GIY-YIG endonuclease	CATH (4.3.0)
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, B, C, D	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, B, C, D	UvrC	excinuclease ABC activity DNA endonuclease activity endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity DNA binding binding 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 nucleotide-excision repair DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair 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 nucleotide-excision repair DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair SOS response	protein-containing complex catalytic complex excinuclease repair complex endodeoxyribonuclease complex intracellular protein-containing complex endonuclease complex DNA repair complex cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004791	UvrABC system, subunit C	Family
A, B, C, D	IPR050066	UvrABC system protein C	Family
A, B, C, D	IPR036876	UVR domain superfamily	Homologous Superfamily
A, B, C, D	IPR001162	UvrC, RNAse H endonuclease domain	Domain
A, B, C, D	IPR010994	RuvA domain 2-like	Homologous Superfamily
A, B, C, D	IPR038476	UvrC, RNAse H endonuclease domain superfamily	Homologous Superfamily
A, B, C, D	IPR001943	UVR domain	Domain
A, B, C, D	IPR047296	UvrC/Cho-like, GIY-YIG domain	Domain
A, B, C, D	IPR035901	GIY-YIG endonuclease superfamily	Homologous Superfamily
A, B, C, D	IPR000305	GIY-YIG endonuclease	Domain

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.