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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE (EC 6.1.1.2) (TRYPTOPHAN-TRNA LIGASE)(TRPRS) (TM0492) FROM THERMOTOGA MARITIMA AT 2.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  17 Feb 06  (Deposition) - 28 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tm0492, Tryptophanyl-Trna Synthetase (Ec 6. 1. 1. 2) (Tryptophan-Trna Ligase)(Trprs), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. W. Han, X. L. Yang, D. Mcmullan, Y. E. Chong, S. S. Krishna, C. L. Rife, D. Weekes, S. M. Brittain, P. Abdubek, E. Ambing, T. Astakhova, H. L. Axelrod, D. Carlton, J. Caruthers, H. J. Chiu, T. Clayton, L. Duan J. Feuerhelm, J. C. Grant, S. K. Grzechnik, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, A. Kumar, D. Marciano, M. D. Miller, A. T. Morse E. Nigoghossian, L. Okach, J. Paulsen, R. Reyes, H. Van Den Bedem, A. White, G. Wolf, Q. Xu, K. O. Hodgson, J. Wooley, A. M. Deacon, A. Godzik, S. A. Lesley, M. A. Elsliger, P. Schimmel, I. A. Wilson
Structure Of A Tryptophanyl-Trna Synthetase Containing An Iron-Sulfur Cluster.
Acta Crystallogr. , Sect. F V. 66 1326 2010
PubMed-ID: 20944229  |  Reference-DOI: 10.1107/S1744309110037619

(-) Compounds

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRPS
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: TRYPTOPHAN-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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1SF41Ligand/IonIRON/SULFUR CLUSTER
2TRP1Mod. Amino AcidTRYPTOPHAN
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1SF42Ligand/IonIRON/SULFUR CLUSTER
2TRP2Mod. Amino AcidTRYPTOPHAN

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:220 , ASP A:221 , ARG A:224 , CYS A:236 , VAL A:238 , CYS A:259 , CYS A:266 , CYS A:269BINDING SITE FOR RESIDUE SF4 A 400
2AC2SOFTWARELEU A:4 , SER A:5 , GLY A:6 , ARG A:8 , HIS A:43 , TYR A:129 , GLN A:133 , ASP A:136 , ILE A:137 , VAL A:145 , GLN A:151 , HOH A:411BINDING SITE FOR RESIDUE TRP A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G36)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G36)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G36)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYW_THEMA9-18  1A:9-18
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYW_THEMA9-18  2A:9-18

(-) Exons   (0, 0)

(no "Exon" information available for 2G36)

(-) 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:323
 aligned with SYW_THEMA | Q9WYW2 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:330
                             1                                                                                                                                                                                                                                                                                                                                    328 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319        |-
            SYW_THEMA     - -MRILSGMRPTGKLHIGHLVGALENWVKLQEEGNECFYFVADWHALTTHYDDVSKLKEYTRDLVRGFLACGIDPEKSVIFVQSGVKEHAELALLFSMIVSVSRLERVPTYKEIKSELNYKDLSTAGFLIYPVLQAADILIYKAEGVPVGEDQVYHIELTREIARRFNYLYDEVFPEPEAILSRVPKLPGTDGRKMSKSYGNIINLEISEKELEQTILRMMTDPARVRRSDPGNPENCPVWKYHQAFDISEEESKWVWEGCTTASIGCVDCKKLLLKNMKRKLAPIWENFRKIDEDPHYVDDVIMEGTKKAREVAAKTMEEVRRAMNLMF-   -
               SCOP domains d2g36a_ A: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhh....hhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhh.-------...hhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhh.......eeee..............hhhhh.......hhhhhhhhhhh..............hhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2g36 A   0 HMRILSGMRPTGKLHIGHLVGALENWVKLQEEGNECFYFVADWHALTTHYDDVSKLKEYTRDLVRGFLACGIDPEKSVIFVQSGVKEHAELALLFSMIVSVSRLERVPTYKEI-------DLSTAGFLIYPVLQAADILIYKAEGVPVGEDQVYHIELTREIARRFNYLYDEVFPEPEAILSRVPKLPGTDGRKMSKSYGNIINLEISEKELEQTILRMMTDPARVRRSDPGNPENCPVWKYHQAFDISEEESKWVWEGCTTASIGCVDCKKLLLKNMKRKLAPIWENFRKIDEDPHYVDDVIMEGTKKAREVAAKTMEEVRRAMNLMFW 401
                                     9        19        29        39        49        59        69        79        89        99       109  |      -|      129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       401
                                                                                                                                          112     120                                                                                                                                                                                                             328|
                                                                                                                                                                                                                                                                                                                                                                   401
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G36)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G36)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYW_THEMA | Q9WYW2)
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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