2QCD

Crystal structure of the orotidine-5'-monophosphate decarboxylase domain of human UMP synthase bound to UMP

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

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	8065848	3000216	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8065848	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	OMPdecase	e2qcdA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: OMPdecase	ECOD (1.6)
B	OMPdecase	e2qcdB1	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)
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	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
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	Uridine 5'-monophosphate synthase (UMP synthase)	pentosyltransferase activity glycosyltransferase activity transferase activity orotate phosphoribosyltransferase activity catalytic activity identical protein binding protein binding binding orotidine-5'-phosphate decarboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase 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 small molecule metabolic process metabolic process pyrimidine-containing compound biosynthetic process ribose phosphate metabolic process pyrimidine nucleoside diphosphate 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 small molecule metabolic process metabolic process pyrimidine-containing compound biosynthetic process ribose phosphate metabolic process pyrimidine nucleoside diphosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process UDP metabolic process nucleoside diphosphate biosynthetic process ribonucleotide biosynthetic process ribonucleotide metabolic process pyrimidine ribonucleoside diphosphate metabolic process ribonucleoside diphosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process cellular metabolic process pyrimidine ribonucleoside diphosphate biosynthetic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside diphosphate metabolic process UDP biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyrimidine nucleoside diphosphate biosynthetic process nucleoside phosphate biosynthetic process cellular process pyrimidine nucleotide biosynthetic process ribonucleoside diphosphate biosynthetic process pyrimidine ribonucleotide biosynthetic process UMP biosynthetic process ribonucleoside monophosphate metabolic process UMP metabolic process nucleoside monophosphate metabolic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process nucleoside monophosphate biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process multi-multicellular organism process multicellular organismal process reproductive process female pregnancy multi-organism reproductive process developmental process regulation of body fluid levels secretion transport mammary gland development gland development animal organ development biological regulation establishment of localization body fluid secretion localization anatomical structure development lactation regulation of biological quality 'de novo' pyrimidine nucleobase biosynthetic process cellular response to stimulus cellular response to chemical stimulus response to stimulus response to chemical cellular response to xenobiotic stimulus response to xenobiotic stimulus 'de novo' UMP biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B	Uridine 5'-monophosphate synthase (UMP synthase)	pentosyltransferase activity glycosyltransferase activity transferase activity orotate phosphoribosyltransferase activity catalytic activity identical protein binding protein binding binding orotidine-5'-phosphate decarboxylase activity carboxy-lyase activity lyase activity carbon-carbon lyase 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 small molecule metabolic process metabolic process pyrimidine-containing compound biosynthetic process ribose phosphate metabolic process pyrimidine nucleoside diphosphate 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 small molecule metabolic process metabolic process pyrimidine-containing compound biosynthetic process ribose phosphate metabolic process pyrimidine nucleoside diphosphate metabolic process nucleotide biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process UDP metabolic process nucleoside diphosphate biosynthetic process ribonucleotide biosynthetic process ribonucleotide metabolic process pyrimidine ribonucleoside diphosphate metabolic process ribonucleoside diphosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process cellular metabolic process pyrimidine ribonucleoside diphosphate biosynthetic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside diphosphate metabolic process UDP biosynthetic process organophosphate metabolic process organophosphate biosynthetic process pyrimidine nucleoside diphosphate biosynthetic process nucleoside phosphate biosynthetic process cellular process pyrimidine nucleotide biosynthetic process ribonucleoside diphosphate biosynthetic process pyrimidine ribonucleotide biosynthetic process UMP biosynthetic process ribonucleoside monophosphate metabolic process UMP metabolic process nucleoside monophosphate metabolic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process nucleoside monophosphate biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process multi-multicellular organism process multicellular organismal process reproductive process female pregnancy multi-organism reproductive process developmental process regulation of body fluid levels secretion transport mammary gland development gland development animal organ development biological regulation establishment of localization body fluid secretion localization anatomical structure development lactation regulation of biological quality 'de novo' pyrimidine nucleobase biosynthetic process cellular response to stimulus cellular response to chemical stimulus response to stimulus response to chemical cellular response to xenobiotic stimulus response to xenobiotic stimulus 'de novo' UMP biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A	IPR000836	Phosphoribosyltransferase domain	Domain
A	IPR001754	Orotidine 5'-phosphate decarboxylase domain	Domain
A	IPR004467	Orotate phosphoribosyl transferase domain	Domain
A	IPR014732	Orotidine 5'-phosphate decarboxylase	Family
A	IPR018089	Orotidine 5'-phosphate decarboxylase, active site	Active Site
A	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A	IPR023031	Orotate phosphoribosyltransferase	Family
A	IPR029057	Phosphoribosyltransferase-like	Homologous Superfamily
B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
B	IPR000836	Phosphoribosyltransferase domain	Domain
B	IPR001754	Orotidine 5'-phosphate decarboxylase domain	Domain
B	IPR004467	Orotate phosphoribosyl transferase domain	Domain
B	IPR014732	Orotidine 5'-phosphate decarboxylase	Family
B	IPR018089	Orotidine 5'-phosphate decarboxylase, active site	Active Site
B	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
B	IPR023031	Orotate phosphoribosyltransferase	Family
B	IPR029057	Phosphoribosyltransferase-like	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P11172	orotic aciduria squamous cell carcinoma inherited aplastic anemia beta thalassemia sickle cell anemia hereditary spherocytosis acute erythroid leukemia breast carcinoma colorectal cancer gastric cancer malignant colon neoplasm breast cancer hepatocellular carcinoma prostate cancer Hereditary orotic aciduria, type 1 orotic aciduria squamous cell carcinoma inherited aplastic anemia beta thalassemia sickle cell anemia hereditary spherocytosis acute erythroid leukemia breast carcinoma colorectal cancer gastric cancer malignant colon neoplasm breast cancer hepatocellular carcinoma prostate cancer Hereditary orotic aciduria, type 1 malignant ependymoma benign colon neoplasm oral cavity neoplasm glioblastoma pituitary cancer hereditary diffuse gastric adenocarcinoma hereditary persistence of fetal hemoglobin intellectual disability lung cancer malignant glioma acute myeloid leukemia carpal tunnel syndrome myocardial infarction colorectal carcinoma ovarian cancer heart disease primitive neuroectodermal tumor thalassemia minor large cell medulloblastoma malignant mesothelioma atypical teratoid rhabdoid tumor medulloblastoma colonic neoplasm non-small cell lung carcinoma gastric neoplasm pilocytic astrocytoma
B	Pharos: P11172	orotic aciduria squamous cell carcinoma inherited aplastic anemia beta thalassemia sickle cell anemia hereditary spherocytosis acute erythroid leukemia breast carcinoma colorectal cancer gastric cancer malignant colon neoplasm breast cancer hepatocellular carcinoma prostate cancer Hereditary orotic aciduria, type 1 orotic aciduria squamous cell carcinoma inherited aplastic anemia beta thalassemia sickle cell anemia hereditary spherocytosis acute erythroid leukemia breast carcinoma colorectal cancer gastric cancer malignant colon neoplasm breast cancer hepatocellular carcinoma prostate cancer Hereditary orotic aciduria, type 1 malignant ependymoma benign colon neoplasm oral cavity neoplasm glioblastoma pituitary cancer hereditary diffuse gastric adenocarcinoma hereditary persistence of fetal hemoglobin intellectual disability lung cancer malignant glioma acute myeloid leukemia carpal tunnel syndrome myocardial infarction colorectal carcinoma ovarian cancer heart disease primitive neuroectodermal tumor thalassemia minor large cell medulloblastoma malignant mesothelioma atypical teratoid rhabdoid tumor medulloblastoma colonic neoplasm non-small cell lung carcinoma gastric neoplasm pilocytic astrocytoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSS	Parent Component: CYS RESID: AA0269 PSI-MOD : L-cysteine persulfide MOD:00274

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.