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(-) Description

Authors :  Y. Yu, Y. Liu, N. Shen, X. Xu, J. Jia, Y. Jin, E. Arnold, J. Ding
Date :  05 Oct 03  (Deposition) - 06 Jul 04  (Release) - 13 Jul 11  (Revision)
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossmann Fold, Four Helix Bundle, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  Y. Yu, Y. Liu, N. Shen, X. Xu, F. Xu, J. Jia, Y. Jin, E. Arnold, J. Ding
Crystal Structure Of Human Tryptophanyl-Trna Synthetase Catalytic Fragment
J. Biol. Chem. V. 279 8378 2004
PubMed-ID: 14660560  |  Reference-DOI: 10.1074/JBC.M311284200

(-) Compounds

    EC Number6.1.1.2
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A(+)
    Expression System StrainBL21(DE3) CODON-PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1O5T)

(-) Sites  (0, 0)

(no "Site" information available for 1O5T)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O5T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O5T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036466E455DSYWC_HUMANUnclassified  ---AE455D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036466E455DSYWC_HUMANUnclassified  ---AE455D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYWC_HUMAN164-174  1A:164-174
Biological Unit 1 (1, 2)
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYWC_HUMAN164-174  2A:164-174

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:378
 aligned with SYWC_HUMAN | P23381 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:378
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463        
               SCOP domains d1o5ta_ A: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1o5tA01 A:94-350 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                           1o5tA02 A:351-471 Tyrosyl-Transfer RNA Synthetase                                                                         CATH domains
               Pfam domains ---------------------------------------------------------tRNA-synt_1b-1o5tA01 A:151-443                                                                                                                                                                                                                                                                       ---------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D---------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------AA_TRNA_LIG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4    -----------------------------------Exon 1.6  PDB: A:141-181 UniProt: 141-181------------------------------------------------------------Exon 1.8  PDB: A:242-276           -------------------------------------Exon 1.10  PDB: A:314-371 UniProt: 314-371                Exon 1.11  PDB: A:372-418 UniProt: 372-418     Exon 1.12b  PDB: A:419-471 UniProt: 419-471           Transcript 1 (1)
           Transcript 1 (2) -----------Exon 1.5  PDB: A:105-141             ---------------------------------------Exon 1.7  PDB: A:181-242 UniProt: 181-242                     ---------------------------------Exon 1.9  PDB: A:276-313              -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
Clan: HUP (230)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYWC_HUMAN | P23381)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004812    aminoacyl-tRNA ligase activity    Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
    GO:0016874    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.
    GO:0000166    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.
    GO:0005515    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).
    GO:0004830    tryptophan-tRNA ligase activity    Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0045765    regulation of angiogenesis    Any process that modulates the frequency, rate or extent of angiogenesis.
    GO:0006418    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.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA 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 or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006436    tryptophanyl-tRNA aminoacylation    The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A 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.
    GO:0005634    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.


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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

        SYWC_HUMAN | P233811r6t 1r6u 1ulh 2ake 2azx 2dr2 2quh 2qui 2quj 2quk

(-) Related Entries Specified in the PDB File

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