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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8039853	3000216	SCOP2B (2022-06-29)
A	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)
B	OMPdecase	e1q6lB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: OMPdecase	ECOD (1.6)
A	OMPdecase	e1q6lA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: OMPdecase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	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	pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process 'de novo' pyrimidine nucleobase biosynthetic process small molecule metabolic process metabolic process pyrimidine-containing compound biosynthetic process monosaccharide metabolic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic 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 lactone metabolic process cellular process small molecule catabolic process monosaccharide 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 EC: 4.1.1.85 (UniProt) Search M-CSA Motif + EC 4.1.1.85

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.