1MC8 | pdb_00001mc8

Crystal Structure of Flap Endonuclease-1 R42E mutant from Pyrococcus horikoshii

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	d1mc8b1	All alpha proteins	SAM domain-like	5' to 3' exonuclease, C-terminal subdomain	5' to 3' exonuclease, C-terminal subdomain	Flap endonuclease-1 (Fen-1 nuclease)	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d1mc8b2	Alpha and beta proteins (a/b)	PIN domain-like	PIN domain-like	5' to 3' exonuclease catalytic domain	Flap endonuclease-1 (Fen-1 nuclease)	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d1mc8a1	All alpha proteins	SAM domain-like	5' to 3' exonuclease, C-terminal subdomain	5' to 3' exonuclease, C-terminal subdomain	Flap endonuclease-1 (Fen-1 nuclease)	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d1mc8a2	Alpha and beta proteins (a/b)	PIN domain-like	PIN domain-like	5' to 3' exonuclease catalytic domain	Flap endonuclease-1 (Fen-1 nuclease)	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	5' to 3' exonuclease, C-terminal subdomain	8043470	3000537	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PIN domain-like	8043472	3001041	SCOP2B (2022-06-29)
A	SCOP2 Family	5' to 3' exonuclease, C-terminal subdomain	8031092	4001035	SCOP2 (2022-06-29)
A	SCOP2 Family	FEN1 catalytic domain-like	8031094	4000504	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	5' to 3' exonuclease, C-terminal subdomain	8043470	3000537	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PIN domain-like	8043472	3001041	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	5_3_exonuc_1	e1mc8B1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: 5_3_exonuc_1	ECOD (1.6)
B	XPG_I	e1mc8B2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: XPG_I	ECOD (1.6)
A	5_3_exonuc_1	e1mc8A1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: 5_3_exonuc_1	ECOD (1.6)
A	XPG_I	e1mc8A2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: XPG_I	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.40.50.1010	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	5'-nuclease	CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00867	XPG I-region (XPG_I)	XPG I-region	-	Family
A, B	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
A, B	Flap Endonuclease-1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding 5'-flap endonuclease activity endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity DNA nuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters catalytic activity 5'-3' exonuclease activity exonuclease activity	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 replication, removal of RNA primer 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 replication, removal of RNA primer catabolic process RNA metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process DNA replication nucleic acid catabolic process RNA catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006086	XPG-I domain	Domain
A, B	IPR023426	Flap endonuclease 1	Family
A, B	IPR029060	PIN-like domain superfamily	Homologous Superfamily
A, B	IPR036279	5'-3' exonuclease, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR008918	Helix-hairpin-helix motif, class 2	Conserved Site
A, B	IPR019974	XPG conserved site	Conserved Site
A, B	IPR006085	XPG, N-terminal	Domain
A, B	IPR019973	Flap endonuclease, archaea	Family
A, B	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.