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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE COMPLEXED WITH SERINE
 
Authors :  A. C. Dock-Bregeon, B. Rees, A. Torres-Larios, G. Bey, J. Caillet, D. Moras
Date :  08 Jun 04  (Deposition) - 30 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.46
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. C. Dock-Bregeon, B. Rees, A. Torres-Larios, G. Bey, J. Caillet, D. Moras
Achieving Error-Free Translation; The Mechanism Of Proofreading Of Threonyl-Trna Synthetase At Atomic Resolution.
Mol. Cell V. 16 375 2004
PubMed-ID: 15525511  |  Reference-DOI: 10.1016/J.MOLCEL.2004.10.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THREONYL-TRNA SYNTHETASE
    ChainsA
    EC Number6.1.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET28
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentDOMAINS N1 AND N2 (RESIDUES 1-224)
    GeneTHRS, B1719, C2116, SF1512, S1630
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymTHREONINE--TRNA LIGASE, THRRS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SER1Mod. Amino AcidSERINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:73 , ALA A:76 , HIS A:77 , ILE A:94 , GLY A:95 , TYR A:104 , ASP A:180 , MET A:181 , CYS A:182 , HOH A:698 , HOH A:887BINDING SITE FOR RESIDUE SER A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:184 -Pro A:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TKE)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TKE)

(-) Sequences/Alignments

Asymmetric/Biological 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:225
 aligned with SYT_ECOLI | P0A8M3 from UniProtKB/Swiss-Prot  Length:642

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
            SYT_ECOLI     1 MPVITLPDGSQRHYDHAVSPMDVALDIGPGLAKACIAGRVNGELVDACDLIENDAQLSIITAKDEEGLEIIRHSCAHLLGHAIKQLWPHTKMAIGPVIDNGFYYDVDLDRTLTQEDVEALEKRMHELAEKNYDVIKKKVSWHEARETFANRGESYKVSILDENIAHDDKPGLYFHEEYVDMCRGPHVPNMRFCHHFKLMKTAGAYWRGDSNNKMLQRIYGTAWADK 226
               SCOP domains d1tkea1 A:1-62                                                d1tkea2 A:63-224 Threonyl-tRNA synthetase (ThrRS), second 'additional' domain                                                                                     -- SCOP domains
               CATH domains 1tkeA01 A:1-64  [code=3.10.20.30, no name defined]              1tkeA02 A:65-129,A:188-224                                       1tkeA03 A:130-187  [code=3.30.54.20, no name defined]     1tkeA02 A:65-129,A:188-224           -- CATH domains
               Pfam domains TGS-1tkeA01 A:1-61                                           -------------------------------------------------------------------------------------------------------------tRNA_SAD-1tkeA02 A:171-219                       ------- Pfam domains
         Sec.struct. author ..eee.....eee.....hhhhhhhhhhhhhhhhh.eeee..eeee........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhh...ee....ee..eeeeeee.....hhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhh.hhhhhhhhhhhh......eeeee..eeeee......hhhhh..eeeeeeeeee.hhh....eeeeeeeee..-. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tke A   1 MPVITLPDGSQRHYDHAVSPMDVALDIGPGLAKACIAGRVNGELVDACDLIENDAQLSIITAKDEEGLEIIRHSCAHLLGHAIKQLWPHTKMAIGPVIDNGFYYDVDLDRTLTQEDVEALEKRMHELAEKNYDVIKKKVSWHEARETFANRGESYKVSILDENIAHDDKPGLYFHEEYVDMCRGPHVPNMRFCHHFKLMKTAGAYWRGDSNNKMLQRIYGTAWA-S 500
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   | |
                                                                                                                                                                                                                                                         224 |
                                                                                                                                                                                                                                                           500

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Ubiquitin (279)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYT_ECOLI | P0A8M3)
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:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004829    threonine-tRNA ligase activity    Catalysis of the reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr).
    GO:0000900    translation repressor activity, nucleic acid binding    Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0045947    negative regulation of translational initiation    Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYT_ECOLI | P0A8M31evk 1evl 1fyf 1kog 1qf6 1tje 1tkg 1tky 4hwo 4hwp 4hwr 4hws 4p3o 4p3p

(-) Related Entries Specified in the PDB File

1qf6 THREONYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(THR)
1tje THE SAME PROTEIN DOMAINS IN THE APO FORM
1tkg
1tky