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Crystal Structure of the Phosphoryl Transfer Transition State Mimic in the Adenylate Kinase: ADP/AlF4/AMP in the active site
Biology and Chemistry Report
3SR0
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSFERASE
    Text Phosphoryl Transfer analogue, AlF4, transferase (Phosphotransferase), phosphoryl transfer, Nucleotide-binding, Phosphoryl Transfer of nucleotides, TRANSFERASE

    Polymeric Molecules

    Chain A,B
    Description Adenylate kinase 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23269.3 
    Source Method genetically manipulated  
    Entity Name AK, ATP-AMP transphosphorylase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ADP  ADENOSINE-5'-DIPHOSPHATE  C10 H15 N5 O10 P2   427.20  View 
    ALF  TETRAFLUOROALUMINATE ION  Al F4   102.98  View 
    AMP  ADENOSINE MONOPHOSPHATE  C10 H14 N5 O7 P   347.22  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B KAD_AQUAE O66490     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  2.7.4.3      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6139   Nucleobase Containing Compound Metabolic Process  Any Cellular Metabolic Process Involving Nucleobases Nucleosides Nucleotides and Nucleic Acids. 
    9165   Nucleotide Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Nucleotides Any Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Glycose Moiety; May Be Mono Di or Triphosphate; This Definition Includes Cyclic Nucleotides (nucleoside Cyclic Phosphates). 
    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. 
    44209   AMP Salvage  The Chemical Reactions and Pathways Resulting in the Formation of Adenosine Monophosphate (amp) From Derivatives of It (either Adenine Adp or Adenosine 3' 5' Bisphosphate) Without De Novo Synthesis. 
    46939   Nucleotide Phosphorylation  The Process of Introducing One or More Phosphate Groups Into a Nucleotide to Produce a Phosphorylated Nucleoside. 
    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. 
    4017   Adenylate Kinase Activity  Catalysis of the Reaction: ATP + AMP = 2 Adp. 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    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. 
    19205   Nucleobase Containing Compound Kinase Activity  Catalysis of the Transfer of a Phosphate Group Usually From ATP or GTP to a Nucleobase Nucleoside Nucleotide or Polynucleotide Substrate. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Scientific Name Aquifex aeolicus  
    Gene adk, aquifex, aq_078
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET3a


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 1192503     adenylate kinase KAD