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crystal structure of human galactokinase complexed with MgAMPPNP and galactose
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE
    Text galactosemia, GHMP superfamily, kinase, TRANSFERASE

    Polymeric Molecules

    Chain A,B,C,D
    Description Galactokinase 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 43641.6 
    Source Method genetically manipulated  
    Entity Name Galactose kinase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GLA  ALPHA D-GALACTOSE  C6 H12 O6   180.16  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D GALK1_HUMAN P51570     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    A B C D        
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    GO ID   Ontology GO Term Definition
    5975   Carbohydrate Metabolic Process  The Chemical Reactions and Pathways Involving Carbohydrates Any of a Group of Organic Compounds Based of the General Formula Cx(h2o)y. Includes the Formation of Carbohydrate Derivatives by the Addition of a Carbohydrate Residue to Another Molecule. 
    6012   Galactose Metabolic Process  The Chemical Reactions and Pathways Involving Galactose the Aldohexose Galacto Hexose. D Galactose Is Widely Distributed in Combined Form in Plants Animals and Microorganisms As a Constituent of Oligo and Polysaccharides; It Also Occurs in Galactolipids and As Its Glucoside in Lactose and Melibiose. 
    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. 
    16310   Phosphorylation  The Process of Introducing a Phosphate Group Into a Molecule Usually with the Formation of a Phosphoric Ester a Phosphoric Anhydride or a Phosphoric Amide. 
    19388   Galactose Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Galactose the Aldohexose Galacto Hexose. 
    19402   Galactitol Metabolic Process  The Chemical Reactions and Pathways Involving Galactitol the Hexitol Derived by the Reduction of the Aldehyde Group of Either D or L Galactose. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    46835   Carbohydrate Phosphorylation  The Process of Introducing a Phosphate Group Into a Carbohydrate Any Organic Compound Based On the General Formula Cx(h2o)y. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    16020   Membrane  A Lipid Bilayer Along with All the Proteins and Protein Complexes Embedded in It an Attached to It. 
    70062   Extracellular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. Extracellular Exosomes Also Simply Called Exosomes Have a Diameter of About 40 100 Nm. 
    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. 
    4335   Galactokinase Activity  Catalysis of the Reaction: D Galactose + ATP = Alpha D Galactose 1 Phosphate + Adp + 2 H(+). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    5534   Galactose Binding  Interacting Selectively and Non Covalently with the Aldohexose Galactose (galacto Hexose) a Common Constituent of Many Oligo and Polysaccharides. 
    16301   Kinase Activity  Catalysis of the Transfer of a Phosphate Group Usually From ATP to a Substrate Molecule. 
    16740   Transferase Activity  Catalysis of the Transfer of a Group E.g. a Methyl Group Glycosyl Group Acyl Group Phosphorus Containing or Other Groups From One Compound (generally Regarded As the Donor) to Another Compound (generally Regarded As the Acceptor). Transferase Is the Systematic Name For Any Enzyme of EC Class 2. 
    16773   Phosphotransferase Activity Alcohol Group As Acceptor  Catalysis of the Transfer of a Phosphorus Containing Group From One Compound (donor) to an Alcohol Group (acceptor). 

  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Genus Homo
    Gene galk1
    Host Scientific Name Escherichia coli  
    Host Genus Escherichia
    Host Strain Hms174(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET15

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    17 17q24 2584     galactokinase 1 GALK1    

    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
    rs104894572 LS-SNP   dbSNP   A 28 P - > T Coil 8% (Buried) 17 73761136
    rs104894576 LS-SNP   dbSNP   A 32 V - > M Beta Ladder 0% (Buried) 17 73761124
    rs146045315 LS-SNP   dbSNP   A 54 P - > R Beta Ladder 0% (Buried) 17 73761057
    rs144915547 LS-SNP   dbSNP   A 89 Q - > H Beta Ladder 61% (Exposed) 17 73760066
    rs149506556 LS-SNP   dbSNP   A 91 P - > L Beta Ladder 43% (Exposed) 17 73760061
    rs140148059 LS-SNP   dbSNP   A 148 A - > T Helix 0% (Buried) 17 73759434
    rs145732791 LS-SNP   dbSNP   A 166 R - > H Helix 11% (Intermediate) 17 73759209
    rs80084721 LS-SNP   dbSNP   A 198 A - > V Beta Ladder 0% (Buried) 17 73759113
    rs145837971 LS-SNP   dbSNP   A 240 R - > Q Helix 17% (Intermediate) 17 73758859
    rs149825190 LS-SNP   dbSNP   A 249 A - > V Helix 34% (Intermediate) 17 73758832
    rs77152477 LS-SNP   dbSNP   A 282 V - > G Helix 8% (Buried) 17 73754629
    rs145641205 LS-SNP   dbSNP   A 286 R - > Q Helix 43% (Exposed) 17 73754617
    rs201681295 LS-SNP   dbSNP   A 310 S - > G Helix 0% (Buried) 17 73754546
    rs201972845 LS-SNP   dbSNP   A 312 R - > C Helix 27% (Intermediate) 17 73754540
    rs181526665 LS-SNP   dbSNP   A 312 R - > H Helix 27% (Intermediate) 17 73754539
    rs61735300 LS-SNP   dbSNP   A 341 S - > T Beta Ladder 0% (Buried) 17 73754376
    rs201811960 LS-SNP   dbSNP   A 374 G - > R Bend 45% (Exposed) 17 73754196