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Crystal structure of human orotidine 5'-monophosphate decarboxylase complexed with CMP-N3-oxide
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Text Alpha-Beta Barrel, decarboxylase, LYASE-LYASE INHIBITOR complex

    Polymeric Molecules

    Chain A,B
    Description Uridine 5'-monophosphate synthase 
    Fragment UNP residues 190-480 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 34054.4 
    Source Method genetically manipulated  
    Entity Name UMP synthase, Orotate phosphoribosyltransferase, OPRT, OPRTase, Orotidine 5'-phosphate decarboxylase, ODC, OMPdecase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    16B  N-hydroxycytidine 5'-(dihydrogen phosphate)  C9 H14 N3 O9 P   339.20  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    TKW  5-hydroxycytidine 5'-(dihydrogen phosphate)  C9 H14 N3 O9 P   339.20  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B UMPS_HUMAN P11172     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6207   'de Novo' Pyrimidine Nucleobase Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Pyrimidine Nucleobases 1 3 Diazine Organic Nitrogenous Bases Beginning with the Synthesis of a Pyrimidine Ring From Simpler Precursors. 
    8152   Metabolic Process  The Chemical Reactions and Pathways Including Anabolism and Catabolism by Which Living Organisms Transform Chemical Substances. Metabolic Processes Typically Transform Small Molecules But Also Include Macromolecular Processes Such As DNA Repair and Replication and Protein Synthesis and Degradation. 
    44205   'de Novo' Ump Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Ump Uridine Monophosphate Starting with the Synthesis of (s) Dihydroorotate From Bicarbonate; Ump Biosynthesis May Either Occur Via Reduction by Quinone Nad(+) or Oxygen. 
    3824   Catalytic Activity  Catalysis of a Biochemical Reaction At Physiological Temperatures. in Biologically Catalyzed Reactions the Reactants Are Known As Substrates and the Catalysts Are Naturally Occurring Macromolecular Substances Known As Enzymes. Enzymes Possess Specific Binding Sites For Substrates and Are Usually Composed Wholly or Largely of Protein But RNA That Has Catalytic Activity (ribozyme) Is Often Also Regarded As Enzymatic. 
    4590   Orotidine 5' Phosphate Decarboxylase Activity  Catalysis of the Reaction: H(+) + Orotidine 5' Phosphate = Co(2) + Ump. 

  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene umps, ok/sw-cl.21
    Host Scientific Name Escherichia coli  

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    3 3q13 7372     uridine monophosphate synthetase UMPS    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs201260688 LS-SNP   dbSNP   A 39 G - > S Helix 25% (Intermediate) 3 124456786
    rs200421426 LS-SNP   dbSNP   A 68 S - > C Beta Ladder 5% (Buried) 3 124456874 16B,TKW
    rs140804035 LS-SNP   dbSNP   A 87 S - > N 3/10 Helix 3% (Buried) 3 124456931
    rs111660155 LS-SNP   dbSNP   A 90 M - > V Beta Ladder 0% (Buried) 3 124456939
    rs200305064 LS-SNP   dbSNP   A 97 I - > N 3/10 Helix 5% (Buried) 3 124456961
    rs201047833 LS-SNP   dbSNP   A 129 I - > V Coil 9% (Buried) 3 124457056 16B,TKW
    rs202135467 LS-SNP   dbSNP   A 166 Q - > K Helix 14% (Intermediate) 3 124458951
    rs201332523 LS-SNP   dbSNP   A 174 R - > Q Coil 15% (Intermediate) 3 124458976
    rs200929871 LS-SNP   dbSNP   A 190 T - > S Coil 62% (Exposed) 3 124459024
    rs202158549 LS-SNP   dbSNP   A 197 A - > V Helix 0% (Buried) 3 124459045
    rs201303915 LS-SNP   dbSNP   A 209 V - > A Beta Ladder 2% (Buried) 3 124461033
    rs200479810 LS-SNP   dbSNP   A 229 G - > A Bend 7% (Buried) 3 124461093 16B,TKW
    rs121917891 LS-SNP   dbSNP   A 240 G - > R Bend 19% (Intermediate) 3 124462773
    rs144643225 LS-SNP   dbSNP   A 244 N - > Y Beta 36% (Intermediate) 3 124462785
    rs201516429 LS-SNP   dbSNP   A 250 I - > T Helix 0% (Buried) 3 124462804
    rs138671830 LS-SNP   dbSNP   A 253 R - > Q Bend 35% (Intermediate) 3 124462813
    rs3772809 LS-SNP   dbSNP   A 257 I - > V Beta Ladder 0% (Buried) 3 124462824
    rs142909683 LS-SNP   dbSNP   A 270 R - > P Helix 23% (Intermediate) 3 124462864