5CO8 | pdb_00005co8

Crystal structure of the Holliday junction-resolving enzyme GEN1 (WT) in complex with product DNA and Mg2+ ion

External Resource: Annotation

Domain Annotation: ECOD Classification
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 [auth A]		e5co8A1	A: ACP-like	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: DEAD, DEAD_2	F:	ECOD (20:10:01)
B [auth C]		e5co8C1	A: ACP-like	X: Phage tail fiber protein trimerization domain	H: Phage tail fiber protein trimerization domain	T: DEAD, DEAD_2	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth A]	PF00867	XPG I-region (XPG_I)	XPG I-region	-	Family
D [auth A]	PF18380	Holliday junction resolvase Gen1 C-terminal domain (GEN1_C)	Holliday junction resolvase Gen1 C-terminal domain	This is the C-terminal domain found in GEN1 resolvase. It is composed of three-strand antiparallel beta sheets and four alpha helices [1]. GEN1 protein, a member of the XPG/Rad2 family of structure-selective endonucleases, is specialized for the clea ...	This is the C-terminal domain found in GEN1 resolvase. It is composed of three-strand antiparallel beta sheets and four alpha helices [1]. GEN1 protein, a member of the XPG/Rad2 family of structure-selective endonucleases, is specialized for the cleavage of Holliday junction recombination intermediates [2]. Structural comparison indicates that the C-terminal domain is similar to a series of chromobox homology proteins [1]. Functional analysis indicates that the chromodomain provides an additional DNA binding site necessary for efficient HJ cleavage, and its truncation severely hampers GEN1's catalytic activity [3].	Domain
D [auth A]	PF00752	XPG N-terminal domain (XPG_N)	XPG N-terminal domain	-	Family
B [auth C]	PF00867	XPG I-region (XPG_I)	XPG I-region	-	Family
B [auth C]	PF18380	Holliday junction resolvase Gen1 C-terminal domain (GEN1_C)	Holliday junction resolvase Gen1 C-terminal domain	This is the C-terminal domain found in GEN1 resolvase. It is composed of three-strand antiparallel beta sheets and four alpha helices [1]. GEN1 protein, a member of the XPG/Rad2 family of structure-selective endonucleases, is specialized for the clea ...	This is the C-terminal domain found in GEN1 resolvase. It is composed of three-strand antiparallel beta sheets and four alpha helices [1]. GEN1 protein, a member of the XPG/Rad2 family of structure-selective endonucleases, is specialized for the cleavage of Holliday junction recombination intermediates [2]. Structural comparison indicates that the C-terminal domain is similar to a series of chromobox homology proteins [1]. Functional analysis indicates that the chromodomain provides an additional DNA binding site necessary for efficient HJ cleavage, and its truncation severely hampers GEN1's catalytic activity [3].	Domain
B [auth C]	PF00752	XPG N-terminal domain (XPG_N)	XPG N-terminal domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth H]	DNA (5'-D(TPGPAPGPCPGPGPTPGPGPTPTPGPGP*A)-3')	-	-	-
D [auth A]	Nuclease-like protein	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 cation binding ion binding 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 cation binding ion binding binding metal ion binding small molecule binding 5'-flap endonuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters	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	-
C [auth X]	DNA (5'-D(APGPAPCPTPGPCPAPGPTPTPGPAPGPTPC)-3')	-	-	-
B [auth C]	Nuclease-like protein	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 cation binding ion binding 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 cation binding ion binding binding metal ion binding small molecule binding 5'-flap endonuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters	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	-
A [auth R]	DNA (31-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth A]	IPR041177	Holliday junction resolvase Gen1, C-terminal domain	Domain
D [auth A]	IPR029060	PIN-like domain superfamily	Homologous Superfamily
D [auth A]	IPR006086	XPG-I domain	Domain
D [auth A]	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
D [auth A]	IPR037316	Yen1, H3TH domain	Domain
D [auth A]	IPR006085	XPG, N-terminal	Domain
D [auth A]	IPR006084	XPG/Rad2 endonuclease	Family
B [auth C]	IPR041177	Holliday junction resolvase Gen1, C-terminal domain	Domain
B [auth C]	IPR029060	PIN-like domain superfamily	Homologous Superfamily
B [auth C]	IPR006086	XPG-I domain	Domain
B [auth C]	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
B [auth C]	IPR037316	Yen1, H3TH domain	Domain
B [auth C]	IPR006085	XPG, N-terminal	Domain
B [auth C]	IPR006084	XPG/Rad2 endonuclease	Family

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.