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(-) Description

Title :  CRYSTAL STRUCTURE OF B. STEAROTHERMOPHILUS TRYPTOPHANYL TRNA SYNTHETASE IN COMPLEX WITH ADENOSINE TETRAPHOSPHATE
 
Authors :  P. Retailleau, C. W. Carter Jr.
Date :  12 Feb 07  (Deposition) - 06 Mar 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Aminoacyl-Trna Synthetase, Nucleotide Binding Site, Rossmann Fold, Transition State Analog Inhibitor, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Retailleau, V. Weinreb, M. Hu, C. W. Carter Jr.
Crystal Structure Of Tryptophanyl-Trna Synthetase Complexed With Adenosine-5' Tetraphosphate: Evidence For Distributed Use Of Catalytic Binding Energy In Amino Acid Activation By Class I Aminoacyl-Trna Synthetases.
J. Mol. Biol. V. 369 108 2007
PubMed-ID: 17428498  |  Reference-DOI: 10.1016/J.JMB.2007.01.091

(-) Compounds

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
    ChainsA
    EC Number6.1.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneTRPS
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    SynonymTRYPTOPHAN--TRNA LIGASE, TRPRS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1ANL1Ligand/IonANILINE
2AQP1Ligand/IonADENOSINE-5'-TETRAPHOSPHATE
3CS1Ligand/IonCESIUM ION
4GOL2Ligand/IonGLYCEROL
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1ANL2Ligand/IonANILINE
2AQP2Ligand/IonADENOSINE-5'-TETRAPHOSPHATE
3CS-1Ligand/IonCESIUM ION
4GOL4Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , GLN A:30 , TYR A:33 , GLN A:74BINDING SITE FOR RESIDUE CS A 900
2AC2SOFTWAREGLY A:7 , ILE A:8 , GLN A:9 , SER A:11 , GLY A:17 , ASN A:18 , GLY A:21 , ALA A:22 , LYS A:111 , VAL A:143 , GLY A:144 , ASP A:146 , GLN A:147 , GLY A:180 , ALA A:181 , ILE A:183 , LYS A:192 , MET A:193 , SER A:194 , LYS A:195 , SER A:196 , HOH A:513 , HOH A:541BINDING SITE FOR RESIDUE AQP A 400
3AC3SOFTWAREPHE A:5 , GLY A:7 , VAL A:40 , HIS A:43 , MET A:129 , ASP A:132 , VAL A:143BINDING SITE FOR RESIDUE ANL A 950
4AC4SOFTWARELYS A:218 , THR A:222 , TYR A:265 , GLY A:266 , LYS A:269 , HOH A:553BINDING SITE FOR RESIDUE GOL A 930
5AC5SOFTWAREARG A:60 , TYR A:287 , HIS A:288 , MET A:291BINDING SITE FOR RESIDUE GOL A 940

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OV4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OV4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OV4)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYW_GEOSE10-19  1A:10-19
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYW_GEOSE10-19  2A:10-19

(-) Exons   (0, 0)

(no "Exon" information available for 2OV4)

(-) 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:328
 aligned with SYW_GEOSE | P00953 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:328
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320        
            SYW_GEOSE     1 MKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAAKYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYIGELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMVRKMEQAMGLGRRR 328
               SCOP domains d2ov4a_ A: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2ov4A01 A:1-182,A:294-328 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                       2ov4A02 A:183-293 Tyrosyl-Transfer RNA Synthetase                                                              2ov4A01 A:1-182,A:294-328           CATH domains
               Pfam domains tRNA-synt_1b-2ov4A01 A:1-281                                                                                                                                                                                                                                                             ----------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhhhhheeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhh......ee........................hhhhh.....hhhhhhhhhhhh..............hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ov4 A   1 MKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAALYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYIGELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMVRKMEQAMGLGRRR 328
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320        

   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  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYW_GEOSE | P00953)
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:0004830    tryptophan-tRNA ligase activity    Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
biological process
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYW_GEOSE | P009531d2r 1i6k 1i6l 1i6m 1m83 1mau 1maw 1mb2 3fhj 3fi0 5dk4

(-) Related Entries Specified in the PDB File

1m83 THE SAME PROTEIN COMPLEXED WITH ADENOSINE TRIPHOSPHATE