Annotations: 3NGF

Crystal structure of AP endonuclease, family 2 from Brucella melitensis

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	d3ngfb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
B	d3ngfb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)
A	d3ngfa_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Brucella abortus 2308 ) [TaxId: 359391 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Xylose isomerase-like	8085446	3000560	SCOP2B (2022-06-29)
A	SCOP2 Family	Hypothetical protein YgbM (EC1530)	8085445	4002224	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Xylose isomerase-like	8085446	3000560	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	PBP	e3ngfB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
A	bZIP_Maf	e3ngfA1	A: a/b three-layered sandwiches	X: Cystatin-like	H: Cytochrome b5-like heme/steroid binding domain	T: Cytochrome b5-like heme/steroid binding domain	F: bZIP_Maf	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
A	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
A, 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, B	AP endonuclease, family 2	endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid catalytic activity isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity hydroxypyruvate isomerase activity cation binding ion binding binding metal ion binding small molecule binding	glyoxylate metabolic process oxoacid metabolic process carboxylic acid metabolic process metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process aldehyde metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013022	Xylose isomerase-like, TIM barrel domain	Domain
A, B	IPR050417	Sugar Epimerase/Isomerase	Family
A, B	IPR036237	Xylose isomerase-like superfamily	Homologous Superfamily
A, B	IPR053398	Hydroxypyruvate and 2-oxo-tetronate isomerases	Family
A, B	IPR026040	Hydroxypyruvate isomerase-like	Family

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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.