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Crystal structure of human prolyl-tRNA synthetase in complex with halofuginone and ATP analogue
Biology and Chemistry Report
4HVC
  •   Structure Details   Hide

    Structure Keywords

    Keywords ligase/ligase inhibitor
    Text ligase, ligase-ligase inhibitor complex

    Polymeric Molecules

    Chain A,B
    Description Bifunctional glutamate/proline--tRNA ligase 
    Fragment ProRS part of EPRS (unp residues 1003-1513) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 59064.1 
    Source Method genetically manipulated  
    Entity Name Bifunctional aminoacyl-tRNA synthetase, Cell proliferation-inducing gene 32 protein, Glutamate--tRNA ligase, Glutamyl-tRNA synthetase, GluRS, Proline--tRNA ligase, Prolyl-tRNA synthetase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ANP  PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER  C10 H17 N6 O12 P3   506.20  View 
    HFG  7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one  C16 H17 Br Cl N3 O3   414.68  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B SYEP_HUMAN A0AVA9     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  6.1.1.15      
    A B  6.1.1.17      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6418   TRNA Aminoacylation For Protein Translation  The Synthesis of Aminoacyl TRNA by the Formation of an Ester Bond Between the 3' Hydroxyl Group of the Most 3' Adenosine of the TRNA to Be Used in Ribosome Mediated Polypeptide Synthesis. 
    6433   Prolyl TRNA Aminoacylation  The Process of Coupling Proline to Prolyl TRNA Catalyzed by Prolyl TRNA Synthetase. in TRNA Aminoacylation the Amino Acid Is First Activated by Linkage to AMP and Then Transferred to Either the 2' or the 3' Hydroxyl Group of the 3' Adenosine Residue of the Trna. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    4812   Aminoacyl TRNA Ligase Activity  Catalysis of the Formation of Aminoacyl TRNA From ATP Amino Acid and TRNA with the Release of Diphosphate and Amp. 
    4827   Proline TRNA Ligase Activity  Catalysis of the Reaction: ATP + L Proline + Trna(pro) = AMP + Diphosphate + L Prolyl Trna(pro). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene eprs, glns, pars, qars, qprs, pig32
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 1q41 2058     glutamyl-prolyl-tRNA synthetase EPRS    

    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
    rs5030753 LS-SNP   dbSNP   A 1041 H - > Y Coil 18% (Intermediate) 1 220156710
    rs5030752 LS-SNP   dbSNP   A 1043 I - > V Bend 8% (Buried) 1 220156704
    rs199749320 LS-SNP   dbSNP   A 1046 C - > W Coil 2% (Buried) 1 220156693
    rs146881805 LS-SNP   dbSNP   A 1054 Y - > C Helix 3% (Buried) 1 220156670
    rs141360496 LS-SNP   dbSNP   A 1072 G - > D Turn 54% (Exposed) 1 220156616
    rs148426546 LS-SNP   dbSNP   A 1082 V - > M Beta Ladder 1% (Buried) 1 220156587
    rs139441122 LS-SNP   dbSNP   A 1091 K - > E Coil 35% (Intermediate) 1 220156560
    rs12144752 LS-SNP   dbSNP   A 1107 S - > F Beta Ladder 12% (Intermediate) 1 220156167
    rs200677731 LS-SNP   dbSNP   A 1137 H - > Y 3/10 Helix 41% (Exposed) 1 220154764
    rs199712671 LS-SNP   dbSNP   A 1183 A - > V Helix 21% (Intermediate) 1 220154105
    rs112749480 LS-SNP   dbSNP   A 1217 A - > V Turn 59% (Exposed) 1 220153488
    rs115571989 LS-SNP   dbSNP   A 1262 P - > L Turn 82% (Exposed) 1 220152884
    rs150455059 LS-SNP   dbSNP   A 1269 Y - > C Beta Ladder 27% (Intermediate) 1 220152863
    rs151171519 LS-SNP   dbSNP   A 1299 V - > A Turn 1% (Buried) 1 220152773
    rs145319165 LS-SNP   dbSNP   A 1324 I - > V Helix 38% (Exposed) 1 220152001
    rs144577435 LS-SNP   dbSNP   A 1324 I - > M Helix 38% (Exposed) 1 220151999
    rs144975474 LS-SNP   dbSNP   A 1338 N - > D Turn 89% (Exposed) 1 220151959
    rs143796513 LS-SNP   dbSNP   A 1340 R - > C Coil 36% (Exposed) 1 220151953
    rs147574977 LS-SNP   dbSNP   A 1372 R - > H Helix 26% (Intermediate) 1 220146709
    rs113334654 LS-SNP   dbSNP   A 1372 R - > C Helix 26% (Intermediate) 1 220146710
    rs139413735 LS-SNP   dbSNP   A 1379 F - > L Beta Ladder 0% (Buried) 1 220146689
    rs181250691 LS-SNP   dbSNP   A 1382 V - > I Beta Ladder 5% (Buried) 1 220146680
    rs34559775 LS-SNP   dbSNP   A 1399 T - > N Helix 77% (Exposed) 1 220146628
    rs148671123 LS-SNP   dbSNP   A 1437 L - > V Helix 2% (Buried) 1 220145425
    rs35055527 LS-SNP   dbSNP   A 1481 I - > V Beta Ladder 9% (Intermediate) 1 220142246
    rs199545183 LS-SNP   dbSNP   A 1486 L - > F Bend 56% (Exposed) 1 220142231
    rs186287404 LS-SNP   dbSNP   A 1502 A - > D Coil 16% (Intermediate) 1 220142182