5NHD

Crystal structure of xylose isomerase from Piromyces E2 in complex with 2 Ni2+ ions and xylose

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	d5nhdc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Piromyces sp. E2 ) [TaxId: 73868 ],	SCOPe (2.08)
D	d5nhdd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Piromyces sp. E2 ) [TaxId: 73868 ],	SCOPe (2.08)
A	d5nhda_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Piromyces sp. E2 ) [TaxId: 73868 ],	SCOPe (2.08)
B	d5nhdb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Piromyces sp. E2 ) [TaxId: 73868 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Xylose isomerase-like	8078202	3000560	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Xylose isomerase-like	8078202	3000560	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Xylose isomerase-like	8078202	3000560	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Xylose isomerase-like	8078202	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	AP_endonuc_2	e5nhdC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: AP_endonuc_2	ECOD (1.6)
D	AP_endonuc_2	e5nhdD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: AP_endonuc_2	ECOD (1.6)
A	AP_endonuc_2	e5nhdA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: AP_endonuc_2	ECOD (1.6)
B	AP_endonuc_2	e5nhdB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: AP_endonuc_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
D	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)
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
A, B, C, D	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, C, D	Xylose isomerase	isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity xylose isomerase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	monosaccharide metabolic process catabolic process energy derivation by oxidation of organic compounds organic hydroxy compound metabolic process carbohydrate catabolic process alcohol metabolic process fermentation small molecule metabolic process pentose metabolic process carbohydrate metabolic process cellular metabolic process primary metabolic process generation of precursor metabolites and energy ethanol metabolic process monosaccharide metabolic process catabolic process energy derivation by oxidation of organic compounds organic hydroxy compound metabolic process carbohydrate catabolic process alcohol metabolic process fermentation small molecule metabolic process pentose metabolic process carbohydrate metabolic process cellular metabolic process primary metabolic process generation of precursor metabolites and energy ethanol metabolic process D-xylose metabolic process D-xylose catabolic process D-xylose catabolic process to ethanol metabolic process cellular process monosaccharide catabolic process small molecule catabolic process pentose catabolic process primary alcohol metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013022	Xylose isomerase-like, TIM barrel domain	Domain
A, B, C, D	IPR013452	Xylose isomerase, bacterial-type	Family
A, B, C, D	IPR036237	Xylose isomerase-like superfamily	Homologous Superfamily
A, B, C, D	IPR001998	Xylose isomerase	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.