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Crystal structure of A. aeolicus tRNASec in complex with M. kandleri SerRS
Biology and Chemistry Report
3W3S
  •   Structure Details   Hide

    Structure Keywords

    Keywords LIGASE/RNA
    Text class 2 aminoacyl-tRNA synthetase, transfer RNA, aminoacylation, selenocysteine incorporation, selenium metabolism, LIGASE-RNA complex

    Polymeric Molecules

    Chain A
    Description Type-2 serine--tRNA ligase 
    Mutation R55Y, E58Y, E62Y, R116Y, D118Y, E189R, D193R, E379Y, E383R, E497Y, E499Y 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 62156.1 
    Source Method genetically manipulated  
    Entity Name Seryl-tRNA synthetase, SerRS, Seryl-tRNA(Ser/Sec) synthetase 
    Chain B
    Description selenocysteine tRNA 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polyribonucleotide 
    Formula Weight 31898.1 
    Source Method synthetic  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    PT  PLATINUM (II) ION  Pt   195.08  View 
    SO4  SULFATE ION  O4 S   96.06  View 
    SSA  5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE  C13 H19 N7 O8 S   433.40  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A SYS2_METKA Q8TVD2     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    6.1.1.11      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    6412   Translation  The Cellular Metabolic Process in Which a Protein Is Formed Using the Sequence of a Mature MRNA Molecule to Specify the Sequence of Amino Acids in a Polypeptide Chain. Translation Is Mediated by the Ribosome and Begins with the Formation of a Ternary Complex Between Aminoacylated Initiator Methionine TRNA GTP and Initiation Factor 2 Which Subsequently Associates with the Small Subunit of the Ribosome and an Mrna. Translation Ends with the Release of a Polypeptide Chain From the Ribosome. 
    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. 
    6434   Seryl TRNA Aminoacylation  The Process of Coupling Serine to Seryl TRNA Catalyzed by Seryl 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. 
    16260   Selenocysteine Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Selenocysteine an Essential Component of Glutathione Peroxidase and Some Other Proteins. 
    97056   Selenocysteinyl Trna(sec) Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Selenocysteinyl Trna(sec). This Process Occurs Through the Following Steps: a Unique Serine TRNA with a Uga Recognizing Anticodon Is First Aminoacylated with Serine; This Is Then Phosphorylated by Phosphoseryl Trna[ser]sec Kinase; Lastly Selenium Is Swapped For the Phosphate On the Serine. 
    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. 
    4828   Serine TRNA Ligase Activity  Catalysis of the Reaction: ATP + L Serine + Trna(ser) = AMP + Diphosphate + L Seryl Trna(ser). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    8270   Zinc Ion Binding  Interacting Selectively and Non Covalently with Zinc (zn) Ions. 
    16874   Ligase Activity  Catalysis of the Joining of Two Substances or Two Groups Within a Single Molecule with the Concomitant Hydrolysis of the Diphosphate Bond in ATP or a Similar Triphosphate. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A
    Scientific Name Methanopyrus kandleri  
    Strain AV19
    Gene sers
    Host Scientific Name Escherichia coli  
    Host Strain Rosetta 2(de3)
    Host Vector Type Plasmid
    Host Plasmid Name pET26b


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    - - 1478055     seryl-tRNA synthetase SERS