An Information Portal to 105025 Biological Macromolecular Structures

Human mitochondrial aspartyl-tRNA synthetase
Biology and Chemistry Report
  •   Structure Details   Hide

    Structure Keywords

    Keywords LIGASE
    Text LIGASE

    Polymeric Molecules

    Chain A,B,C,D
    Fragment RESIDUES 41-645 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 70378.5 
    Source Method genetically manipulated  

  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B,C,D SYDM_HUMAN Q6PI48     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B C D      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B,C,D
    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. 
    10467   Gene Expression  The Process in Which a Gene's Sequence Is Converted Into a Mature Gene Product or Products (proteins or Rna). This Includes the Production of an RNA Transcript As Well As Any Processing to Produce a Mature RNA Product or an MRNA (for Protein Coding Genes) and the Translation of That MRNA Into Protein. Some Protein Processing Events May Be Included When They Are Required to Form an Active Form of a Product From an Inactive Precursor Form. 
    43039   TRNA Aminoacylation  The Chemical Reactions and Pathways by Which the Various Amino Acids Become Bonded to Their Corresponding Trnas. the Most Common Route For Synthesis of Aminoacyl TRNA Is by the Formation of an Ester Bond Between the 3' Hydroxyl Group of the Most 3' Adenosine of the TRNA Usually Catalyzed by the Cognate Aminoacyl TRNA Ligase. a Given Aminoacyl TRNA Ligase Aminoacylates All Species of an Isoaccepting Group of TRNA Molecules. 
    70145   Mitochondrial Asparaginyl TRNA Aminoacylation  The Process of Coupling Asparagine to Asparaginyl TRNA in a Mitochondrion Catalyzed by Asparaginyl 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. 
    5634   Nucleus  A Membrane Bounded Organelle of Eukaryotic Cells in Which Chromosomes Are Housed and Replicated. in Most Cells the Nucleus Contains All of the Cell's Chromosomes Except the Organellar Chromosomes and Is the Site of RNA Synthesis and Processing. in Some Species or in Specialized Cell Types RNA Metabolism or DNA Replication May Be Absent. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5739   Mitochondrion  A Semiautonomous Self Replicating Organelle That Occurs in Varying Numbers Shapes and Sizes in the Cytoplasm of Virtually All Eukaryotic Cells. It Is Notably the Site of Tissue Respiration. 
    5759   Mitochondrial Matrix  The Gel Like Material with Considerable Fine Structure That Lies in the Matrix Space or Lumen of a Mitochondrion. It Contains the Enzymes of the Tricarboxylic Acid Cycle and in Some Organisms the Enzymes Concerned with Fatty Acid Oxidation. 
    49   TRNA Binding  Interacting Selectively and Non Covalently with Transfer Rna. 
    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. 
    3676   Nucleic Acid Binding  Interacting Selectively and Non Covalently with Any Nucleic Acid. 
    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. 
    4815   Aspartate TRNA Ligase Activity  Catalysis of the Reaction: ATP + L Aspartate + Trna(asp) = AMP + Diphosphate + L Aspartyl Trna(asp). 
    5515   Protein Binding  Interacting Selectively and Non Covalently with Any Protein or Protein Complex (a Complex of Two or More Proteins That May Include Other Nonprotein Molecules). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    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. 
    42803   Protein Homodimerization Activity  Interacting Selectively and Non Covalently with an Identical Protein to Form a Homodimer. 
    50560   Aspartate Trna(asn) Ligase Activity  Catalysis of the Reaction: Trna(asx) + L Aspartate + ATP = Aspartyl Trna(asx) + Diphosphate + Amp. 

  •   Gene Details   Hide

    Genetic Source

    Chain A,B,C,D
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  
    Host Variant Rosetta 2
    Host Strain Bl21
    Host Plasmid Name PDEST

    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 1q25.1 55157     aspartyl-tRNA synthetase 2, mitochondrial DARS2    

    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
    rs121918209 LS-SNP   dbSNP   A 45 S - > G Bend 7% (Buried) 1 173795830
    rs150167473 LS-SNP   dbSNP   A 50 R - > Q Coil 4% (Buried) 1 173795846
    rs114714497 LS-SNP   dbSNP   A 63 G - > D Turn 65% (Exposed) 1 173795885
    rs202232688 LS-SNP   dbSNP   A 67 T - > I Beta Ladder 25% (Intermediate) 1 173795897
    rs149598381 LS-SNP   dbSNP   A 87 D - > G Bend 39% (Exposed) 1 173797503
    rs121918208 LS-SNP   dbSNP   A 152 C - > F Beta 12% (Intermediate) 1 173800731
    rs199930349 LS-SNP   dbSNP   A 163 V - > M Coil 8% (Buried) 1 173800763
    rs121918210 LS-SNP   dbSNP   A 179 R - > H Turn 4% (Buried) 1 173802557
    rs182811621 LS-SNP   dbSNP   A 188 R - > Q Helix 20% (Intermediate) 1 173802584
    rs186723843 LS-SNP   dbSNP   A 194 V - > I Helix 5% (Buried) 1 173802601
    rs35515638 LS-SNP   dbSNP   A 196 K - > R Helix 15% (Intermediate) 1 173802608
    rs121918207 LS-SNP   dbSNP   A 263 R - > PQ Beta Ladder 15% (Intermediate) 1 173807345
    rs141298312 LS-SNP   dbSNP   A 338 G - > E Coil 55% (Exposed) 1 173808677
    rs200537352 LS-SNP   dbSNP   A 343 D - > G Beta Ladder 42% (Exposed) 1 173810011
    rs138154457 LS-SNP   dbSNP   A 416 N - > D Helix 21% (Intermediate) 1 173819519
    rs150642385 LS-SNP   dbSNP   A 435 E - > D Bend 40% (Exposed) 1 173819578
    rs200522610 LS-SNP   dbSNP   A 466 R - > G Turn 67% (Exposed) 1 173822538
    rs201652519 LS-SNP   dbSNP   A 474 T - > I Turn 66% (Exposed) 1 173822563
    rs149355062 LS-SNP   dbSNP   A 480 W - > G Beta Ladder 1% (Buried) 1 173822580
    rs181672516 LS-SNP   dbSNP   A 484 F - > L Coil 3% (Buried) 1 173822594
    rs146122206 LS-SNP   dbSNP   A 499 S - > W Beta 15% (Intermediate) 1 173822638
    rs201876507 LS-SNP   dbSNP   A 520 K - > Q Turn 32% (Intermediate) 1 173822700
    rs149660059 LS-SNP   dbSNP   A 548 L - > M Helix 21% (Intermediate) 1 173823011
    rs147779891 LS-SNP   dbSNP   A 552 I - > F Helix 6% (Buried) 1 173823023
    rs147603024 LS-SNP   dbSNP   A 554 A - > T Helix 24% (Intermediate) 1 173823029
    rs141483913 LS-SNP   dbSNP   A 588 L - > P Helix 1% (Buried) 1 173826668
    rs200670286 LS-SNP   dbSNP   A 609 R - > W Bend 18% (Intermediate) 1 173826730
    rs121918212 LS-SNP   dbSNP   A 613 L - > F Bend 29% (Intermediate) 1 173826742
    rs121918205 LS-SNP   dbSNP   A 626 L - > V Turn 37% (Exposed) 1 173826781
    rs121918213 LS-SNP   dbSNP   A 626 L - > Q Turn 37% (Exposed) 1 173826782