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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE FROM YERSINIA PESTIS CO92
 
Authors :  B. Nocek, N. Maltseva, L. Papazisi, W. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)
Date :  30 May 10  (Deposition) - 21 Jul 10  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tryptophanyl-Trna Synthetase, Tryptophan-Trna Ligase, Csgid, Structural Genomics, Niaid, Center For Structural Genomics Of Infectious Diseases, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, N. Maltseva, L. Papazisi, W. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Tryptophanyl-Trna Synthetase From Yersinia Pestis Co92
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.2
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 10029
    Expression System Vector Type: PMCSG7
    Gene: TRPS, YPO0157, Y3940, YP_0159
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: TRYPTOPHAN--TRNA LIGASE, TRPRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:21 , VAL A:54 , MET A:144 , ASP A:147BINDING SITE FOR RESIDUE GOL A 1001
2AC2SOFTWAREGLU A:299 , TYR B:247 , HOH B:354 , HOH B:487 , HOH B:515 , HOH B:516BINDING SITE FOR RESIDUE CA B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N9I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:241 -Pro A:242
2Glu B:241 -Pro B:242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N9I)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYW_YERPE20-29
 		  2A:24-33
B:24-33

(-) Exons   (0, 0)

(no "Exon" information available for 3N9I)

(-) 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:332
 aligned with SYW_YERPE | Q8ZJF2 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:332
                                    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       330       340  
            SYW_YERPE    11 KPIVFSGAQPSGELTIGNYMGALRQWVQMQDDYDCIYCIVDLHAITARQDPALLRKRTLDTLALYLACGIDPKKSTIFVQSHVPEHSQLSWALNCYTYFGELSRMTQFKDKSARYAENINAGLFDYPVLMAADILLYQTNQVPVGEDQKQHLELSRDIASRFNNLYGDIFKIPEPFIPKAGARVMSLQDPTKKMSKSDDNRNNVIELLEDPKSVVKKIKRAMTDSDEPALIRYDVEKKAGVSNLLDILSGVTGQSIPELEAQFTGQMYGHLKGAVADAVSGMLSELQERYRTYREDEALLQDVMREGAAKARARAQVTLAKVYEAIGFVAQP 342
               SCOP domains d3n9ia_ A: automated matches                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhh.....eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhh......ee........................hhhhh.....hhhhhhhhhhh.................hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9i A  15 KPIVFSGAQPSGELTIGNYMGALRQWVQMQDDYDCIYCIVDLHAITARQDPALLRKRTLDTLALYLACGIDPKKSTIFVQSHVPEHSQLSWALNCYTYFGELSRMTQFKDKSARYAENINAGLFDYPVLMAADILLYQTNQVPVGEDQKQHLELSRDIASRFNNLYGDIFKIPEPFIPKAGARVMSLQDPTKKMSKSDDNRNNVIELLEDPKSVVKKIKRAMTDSDEPALIRYDVEKKAGVSNLLDILSGVTGQSIPELEAQFTGQMYGHLKGAVADAVSGMLSELQERYRTYREDEALLQDVMREGAAKARARAQVTLAKVYEAIGFVAQP 346
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344  


Chain B from PDB  Type:PROTEIN  Length:332
 aligned with SYW_YERPE | Q8ZJF2 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:332
                                    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       330       340  
            SYW_YERPE    11 KPIVFSGAQPSGELTIGNYMGALRQWVQMQDDYDCIYCIVDLHAITARQDPALLRKRTLDTLALYLACGIDPKKSTIFVQSHVPEHSQLSWALNCYTYFGELSRMTQFKDKSARYAENINAGLFDYPVLMAADILLYQTNQVPVGEDQKQHLELSRDIASRFNNLYGDIFKIPEPFIPKAGARVMSLQDPTKKMSKSDDNRNNVIELLEDPKSVVKKIKRAMTDSDEPALIRYDVEKKAGVSNLLDILSGVTGQSIPELEAQFTGQMYGHLKGAVADAVSGMLSELQERYRTYREDEALLQDVMREGAAKARARAQVTLAKVYEAIGFVAQP 342
               SCOP domains d3n9ib_ B: automated matches                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) tRNA-synt_1b-3n9iB01 B:15-298                                                                                                                                                                                                                                                               ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) tRNA-synt_1b-3n9iB02 B:15-298                                                                                                                                                                                                                                                               ------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhh....eeeeeehhhhhh....hhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhh......ee........................hhhhh.....hhhhhhhhhhh.................hhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LI------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n9i B  15 KPIVFSGAQPSGELTIGNYMGALRQWVQMQDDYDCIYCIVDLHAITARQDPALLRKRTLDTLALYLACGIDPKKSTIFVQSHVPEHSQLSWALNCYTYFGELSRMTQFKDKSARYAENINAGLFDYPVLMAADILLYQTNQVPVGEDQKQHLELSRDIASRFNNLYGDIFKIPEPFIPKAGARVMSLQDPTKKMSKSDDNRNNVIELLEDPKSVVKKIKRAMTDSDEPALIRYDVEKKAGVSNLLDILSGVTGQSIPELEAQFTGQMYGHLKGAVADAVSGMLSELQERYRTYREDEALLQDVMREGAAKARARAQVTLAKVYEAIGFVAQP 346
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N9I)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYW_YERPE | Q8ZJF2)
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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