1Q6L

Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-threonohydroxamate 4-phosphate

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
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1q6la_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	3-keto-L-gulonate 6-phosphate decarboxylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1q6lb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	3-keto-L-gulonate 6-phosphate decarboxylase	(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)
A	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8039853	3000216	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8039853	3000216	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)
A	PF00215	e1q6lA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00215	ECOD (1.6)
B	PF00215	e1q6lB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00215	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00215	Orotidine 5'-phosphate decarboxylase / HUMPS family (OMPdecase)	Orotidine 5'-phosphate decarboxylase / HUMPS family	This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly ...	This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly related to Pfam:PF00834.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	3-keto-L-gulonate 6-phosphate decarboxylase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding 3-dehydro-L-gulonate-6-phosphate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity orotidine-5'-phosphate decarboxylase activity	organonitrogen compound metabolic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process organonitrogen compound biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process organonitrogen compound metabolic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process organonitrogen compound biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process organic cyclic compound biosynthetic process organic substance biosynthetic process 'de novo' pyrimidine nucleobase biosynthetic process small molecule metabolic process metabolic process pyrimidine-containing compound biosynthetic process monosaccharide metabolic process catabolic process oxoacid metabolic process carbohydrate catabolic process organic acid catabolic process organic acid metabolic process L-ascorbic acid metabolic process cellular catabolic process water-soluble vitamin catabolic process carboxylic acid catabolic process lactone catabolic process water-soluble vitamin metabolic process carbohydrate metabolic process cellular metabolic process carboxylic acid metabolic process L-ascorbic acid catabolic process vitamin metabolic process vitamin catabolic process organic cyclic compound catabolic process lactone metabolic process cellular process small molecule catabolic process monosaccharide catabolic process organic substance catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR041710	HPS/KGPDC domain	Domain
A, B	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR001754	Orotidine 5'-phosphate decarboxylase domain	Domain
A, B	IPR023942	3-keto-L-gulonate-6-phosphate decarboxylase, UlaD	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B	3-dehydro-L-gulonate-6-phosphate decarboxylase M-CSA #236	3-keto-L-gulonate 6-phosphate decarboxylase (KGPDC), isolated from Escherichia coli, catalyses the decarboxylation of 3-keto-L-gulonate 6-phosphate to L-xylulose 5-phosphate and carbon dioxide. KGPDB is a member of the orotidine 5'-monophosphate decarboxylase suprafamily, in that it shares a common active site architecture but not substrate specificity or mechanism. KGPDC is promiscuous and can also catalyse a low level of the D-arabino-hex-3-ulose 6-phosphate synthase (HPS) reaction: D-ribulose 5-phosphate and formaldehyde to D-arabino-hex-3-ulose 6-phosphate. KGPDC exists as a homodimer with two active sites. Residues from both subunits can be found in each active site.	Defined by 9 residues: THR:A-36ILE:A-37LYS:A-64GLU:A-112HIS:A-136ARG:A-139ASP:B-67ALA:B-68LEU:B-72 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.1.2 (PDB Primary Data) Search M-CSA Motif + EC 4.1.2

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 R01GM133198.