2NQJ

Crystal structure of Escherichia coli endonuclease IV (Endo IV) E261Q mutant bound to damaged DNA

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)
C [auth A]	d2nqja_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	Endonuclease IV	Endonuclease IV	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth B]	d2nqjb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	Endonuclease IV	Endonuclease IV	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2B Superfamily	Xylose isomerase-like	8043705	3000560	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Xylose isomerase-like	8043705	3000560	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth A]	PF01261	e2nqjA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF01261	ECOD (1.6)
D [auth B]	PF01261	e2nqjB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF01261	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
D [auth B]	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF01261	Xylose isomerase-like TIM barrel (AP_endonuc_2)	Xylose isomerase-like TIM barrel	This TIM alpha/beta barrel structure is found in xylose isomerase (Swiss:P19148) and in endonuclease IV (Swiss:P12638, EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the ...	This TIM alpha/beta barrel structure is found in xylose isomerase (Swiss:P19148) and in endonuclease IV (Swiss:P12638, EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	5'-D(GPCPGPTPCPCP(3DR)PCPGPAPCPGPAPCP*G)-3'	-	-	-
B [auth D]	5'-D(CPGPTPCPGPTPCPGPGPGPGPAPCPGP*C)-3'	-	-	-
C [auth A], D [auth B]	Endonuclease 4	DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity catalytic activity DNA binding DNA exonuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA 3'-5'-DNA exonuclease activity exonuclease activity catalytic activity DNA binding binding organic cyclic compound binding nucleic acid binding endonuclease activity endodeoxyribonuclease activity, producing 5'-phosphomonoesters DNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters deoxyribonuclease IV (phage-T4-induced) activity DNA-(apurinic or apyrimidinic site) endonuclease activity phosphoric ester hydrolase activity phosphoric diester hydrolase activity phosphatase activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus response to stimulus 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 stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process cellular response to stimulus response to stimulus 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 stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair base-excision repair	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR001719	AP endonuclease 2	Family
C [auth A], D [auth B]	IPR036237	Xylose isomerase-like superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR013022	Xylose isomerase-like, TIM barrel domain	Domain
C [auth A], D [auth B]	IPR018246	AP endonuclease 2, zinc binding site	Binding Site

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.