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(-) Description

Title :  SOLUTION STRUCTURE OF THE TGS DOMAIN FROM HUMAN THREONYL-TRNA SYNTHETASE
 
Authors :  E. Chikayama, T. Kigawa, T. Tomizawa, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  18 Jan 05  (Deposition) - 18 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Tgs Domain, Threonyl-Trna Synthetase, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Chikayama, T. Kigawa, T. Tomizawa, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Tgs Domain From Human Threonyl-Trna Synthetase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THREONYL-TRNA SYNTHETASE, CYTOPLASMIC
    Chains: A
    EC Number: 6.1.1.3
    Engineered: YES
    Expression System Plasmid: P040524-03
    Expression System Vector Type: PLASMID
    Fragment: TGS DOMAIN
    Gene: THRS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: THREONINE--TRNA LIGASE, THRRS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1WWT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034533G21DSYTC_HUMANPolymorphism34334786AG1D
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WWT)

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000002651121cENSE00001948035chr5:33440882-33441249368SYTC_HUMAN1-19190--
1.3ENST000002651123ENSE00001774665chr5:33445430-3344551081SYTC_HUMAN20-46271A:1-7 (gaps)23
1.6bENST000002651126bENSE00001602051chr5:33448647-33448837191SYTC_HUMAN47-110641A:8-3932
1.8cENST000002651128cENSE00000735265chr5:33453394-33453517124SYTC_HUMAN110-151421A:39-8042
1.9bENST000002651129bENSE00000735266chr5:33455050-33455171122SYTC_HUMAN152-192411A:81-85 (gaps)26
1.10ENST0000026511210ENSE00000804523chr5:33455692-33455809118SYTC_HUMAN192-231401A:86-883
1.11aENST0000026511211aENSE00001164413chr5:33456107-3345617165SYTC_HUMAN232-253220--
1.12ENST0000026511212ENSE00001164409chr5:33456254-3345633279SYTC_HUMAN253-279270--
1.13ENST0000026511213ENSE00000735270chr5:33457362-33457508147SYTC_HUMAN280-328490--
1.14ENST0000026511214ENSE00000735271chr5:33458671-3345876999SYTC_HUMAN329-361330--
1.15aENST0000026511215aENSE00000735273chr5:33459800-33459966167SYTC_HUMAN362-417560--
1.16aENST0000026511216aENSE00000735275chr5:33461007-33461169163SYTC_HUMAN417-471550--
1.17ENST0000026511217ENSE00000735276chr5:33461263-33461400138SYTC_HUMAN472-517460--
1.18ENST0000026511218ENSE00000735277chr5:33461772-3346184978SYTC_HUMAN518-543260--
1.19ENST0000026511219ENSE00000735278chr5:33462011-33462111101SYTC_HUMAN544-577340--
1.20ENST0000026511220ENSE00000735279chr5:33462204-33462308105SYTC_HUMAN577-612360--
1.21ENST0000026511221ENSE00001082100chr5:33463858-3346393073SYTC_HUMAN612-636250--
1.23cENST0000026511223cENSE00001082102chr5:33466976-33467090115SYTC_HUMAN637-675390--
1.24fENST0000026511224fENSE00001887096chr5:33467665-334696441980SYTC_HUMAN675-723490--

(-) Sequences/Alignments

NMR Structure
   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:88
 aligned with SYTC_HUMAN | P26639 from UniProtKB/Swiss-Prot  Length:723

    Alignment length:177
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
           SYTC_HUMAN    21 GAGEEKQKEGGKKKNKEGSGDGGRAELNPWPEYIYTRLEMYNILKAEHDSILAEKAEKDSKPIKVTLPDGKQVDAESWKTTPYQIACGISQGLADNTVIAKVNNVVWDLDRPLEEDCTLELLKFEDEEAQAVYWHSSAHIMGEAMERVYGGCLCYGPPIENGFYYDMYLEEGGVSSN 197
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------TGS-1wwtA01 A:12-72                                          ------------------------------------------------------ Pfam domains
         Sec.struct. author ..----------------.....-----------------------------------...eeeee.....eeeee....hhhhhhhhh...hhhhh..eee...ee.........eeeee.............---------------------..-----------------... Sec.struct. author
                 SAPs(SNPs) D-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-7 (gapsExon 1.6b  PDB: A:8-39 UniProt: 47-110 [INCOMPLETE]             ---------------------------------------------------------------------------------1.10   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------Exon 1.8c  PDB: A:39-80 UniProt: 110-151  Exon 1.9b  PDB: A:81-85 (gaps)           ----- Transcript 1 (2)
                 1wwt A   1 GS----------------SGSSG-----------------------------------DSKPIKVTLPDGKQVDAESWKTTPYQIACGISQGLADNTVIAKVNNVVWDLDRPLEEDCTLELLKFEDEEAQAVYS---------------------GP-----------------SSG  88
                             |       -        |4  |      -         -         -        |9        19        29        39        49        59        69        79   |     -         -     ||  -         -    |  
                             2                3   7                                   8                                                                         83                    84|                86  
                                                                                                                                                                                       85
   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  (0, 0)

(no "SCOP Domain" information available for 1WWT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WWT)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (17, 17)

NMR Structure(hide GO term definitions)
Chain A   (SYTC_HUMAN | P26639)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0016876    ligase activity, forming aminoacyl-tRNA and related compounds    Catalysis of the joining of an amino acid and a nucleic acid (usually tRNA) or poly(ribitol phosphate), with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. The reaction forms an aminoacyl-tRNA or a related compound.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004829    threonine-tRNA ligase activity    Catalysis of the reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr).
biological process
    GO:0043039    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.
    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:0006435    threonyl-tRNA aminoacylation    The process of coupling threonine to threonyl-tRNA, catalyzed by threonyl-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.
    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.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    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.

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        SYTC_HUMAN | P26639: 4hwt 4p3n 4ttv

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