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Crystal Structure of Human Pyruvate Carboxylase (missing the biotin carboxylase domain at the N-terminus)
Biology and Chemistry Report
3BG3
  •   Structure Details   Hide

    Structure Keywords

    Keywords LIGASE
    Text TIM barrel, ATP-binding, Biotin, Disease mutation, Gluconeogenesis, Ligase, Lipid synthesis, Manganese, Mitochondrion, Multifunctional enzyme, Nucleotide-binding, Phosphoprotein, Transit peptide

    Polymeric Molecules

    Chain A,B,C,D
    Description Pyruvate carboxylase, mitochondrial 
    Fragment CT+PT+BCCP Domain 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 78840.0 
    Source Method genetically manipulated  
    Entity Name Pyruvic carboxylase, PCB 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    BTI  5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL  C10 H16 N2 O2 S   228.31  View 
    MN  MANGANESE (II) ION  Mn   54.94  View 
    PYR  PYRUVIC ACID  C3 H4 O3   88.06  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D PYC_HUMAN P11498     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    A B C D  6.4.1.1        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    GO ID   Ontology GO Term Definition
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    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. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene pc
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Strain Bl21(de3) Star
    Host Vector Type Plasmid
    Host Plasmid Name pET28a


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    11 11q13.4-q13.5 5091     pyruvate carboxylase PC    

    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
    rs45461300 LS-SNP   dbSNP   A 506 H - > Y Helix 22% (Intermediate) 11 66620305
    rs199667095 LS-SNP   dbSNP   A 512 P - > Q Coil 39% (Exposed) 11 66620286
    rs146840773 LS-SNP   dbSNP   A 525 T - > M Bend 20% (Intermediate) 11 66620247
    rs200433873 LS-SNP   dbSNP   A 528 V - > I Coil 36% (Intermediate) 11 66620239
    rs151174961 LS-SNP   dbSNP   A 538 P - > L Coil 42% (Exposed) 11 66620122
    rs142036463 LS-SNP   dbSNP   A 547 R - > Q Helix 85% (Exposed) 11 66620095
    rs45555439 LS-SNP   dbSNP   A 552 G - > D Helix 1% (Buried) 11 66620080
    rs148613404 LS-SNP   dbSNP   A 555 R - > Q Helix 61% (Exposed) 11 66620071
    rs199969388 LS-SNP   dbSNP   A 568 T - > A Coil 0% (Buried) 11 66620033
    rs113994144 LS-SNP   dbSNP   A 569 T - > A Turn 0% (Buried) 11 66620030
    rs119103242 LS-SNP   dbSNP   A 583 R - > L Coil 0% (Buried) 11 66619987
    rs143725101 LS-SNP   dbSNP   A 589 K - > N Helix 53% (Exposed) 11 66619968
    rs139795235 LS-SNP   dbSNP   A 591 A - > T Helix 0% (Buried) 11 66619964
    rs28940589 LS-SNP   dbSNP   A 610 A - > T Turn 10% (Intermediate) 11 66619415 PYR,BTI
    rs147396184 LS-SNP   dbSNP   A 613 D - > V Helix 3% (Buried) 11 66619405 BTI
    rs199568784 LS-SNP   dbSNP   A 625 R - > Q Helix 36% (Exposed) 11 66619369
    rs113994145 LS-SNP   dbSNP   A 631 R - > Q Helix 9% (Intermediate) 11 66619351
    rs138760063 LS-SNP   dbSNP   A 667 K - > T Helix 31% (Intermediate) 11 66618734
    rs185412729 LS-SNP   dbSNP   A 712 D - > N Coil 28% (Intermediate) 11 66618600
    rs193271416 LS-SNP   dbSNP   A 728 E - > K Helix 31% (Intermediate) 11 66618552
    rs112948607 LS-SNP   dbSNP   A 732 R - > G Helix 77% (Exposed) 11 66618540
    rs28940590 LS-SNP   dbSNP   A 743 M - > I Turn 2% (Buried) 11 66618389 KCX,MN
    rs145400751 LS-SNP   dbSNP   A 750 T - > M Helix 38% (Exposed) 11 66618369
    rs148086243 LS-SNP   dbSNP   A 794 V - > L Beta Ladder 0% (Buried) 11 66618238
    rs141730205 LS-SNP   dbSNP   A 830 R - > C Helix 33% (Intermediate) 11 66617921
    rs113994147 LS-SNP   dbSNP   A 847 A - > V 3/10 Helix 8% (Buried) 11 66617869
    rs11550554 LS-SNP   dbSNP   A 867 P - > R Coil 7% (Buried) 11 66617809
    rs139540331 LS-SNP   dbSNP   A 935 A - > V Turn 1% (Buried) 11 66617502
    rs192822072 LS-SNP   dbSNP   A 964 R - > C Helix 13% (Intermediate) 11 66617416
    rs145046106 LS-SNP   dbSNP   A 1003 T - > M Coil 43% (Exposed) 11 66617221
    rs199771464 LS-SNP   dbSNP   A 1009 S - > L Helix 1% (Buried) 11 66617203
    rs200315043 LS-SNP   dbSNP   A 1023 F - > L Helix 10% (Intermediate) 11 66617162
    rs141237842 LS-SNP   dbSNP   A 1036 R - > H Helix 16% (Intermediate) 11 66617122
    rs140320331 LS-SNP   dbSNP   A 1037 L - > H Helix 4% (Buried) 11 66617119
    rs148661980 LS-SNP   dbSNP   A 1057 T - > M Beta Ladder 48% (Exposed) 11 66616819
    rs34376611 LS-SNP   dbSNP   A 1065 V - > G Beta Ladder 37% (Exposed) 11 66616795
    rs149583113 LS-SNP   dbSNP   A 1071 A - > G Turn 54% (Exposed) 11 66616777
    rs148492494 LS-SNP   dbSNP   A 1114 A - > V Coil 1% (Buried) 11 66616566
    rs182440197 LS-SNP   dbSNP   A 1126 V - > M Coil 82% (Exposed) 11 66616531
    rs200217380 LS-SNP   dbSNP   A 1127 A - > V Turn 73% (Exposed) 11 66616527
    rs138990904 LS-SNP   dbSNP   A 1128 G - > A Turn 43% (Exposed) 11 66616524
    rs141118314 LS-SNP   dbSNP   A 1129 A - > DV Coil 34% (Intermediate) 11 66616521
    rs200166901 LS-SNP   dbSNP   A 1130 K - > N Coil 72% (Exposed) 11 66616517
    rs116518022 LS-SNP   dbSNP   A 1131 V - > M Beta 6% (Buried) 11 66616516
    rs201796252 LS-SNP   dbSNP   A 1145 M - > I Coil 5% (Buried) 11 66616472
    rs199640363 LS-SNP   dbSNP   A 1153 M - > V Coil 42% (Exposed) 11 66616450
    rs149054698 LS-SNP   dbSNP   A 1158 R - > H Coil 61% (Exposed) 11 66616434
    rs143777875 LS-SNP   dbSNP   A 1158 R - > G Coil 61% (Exposed) 11 66616435
    rs147594996 LS-SNP   dbSNP   A 1166 M - > T Beta Ladder 84% (Exposed) 11 66616410
    rs141139690 LS-SNP   dbSNP   A 1178 E - > K Coil 69% (Exposed) 11 66616375