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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF S. CEREVISIAE TRYPTOPHANYL TRNA SYNTHETASE
 
Authors :  M. G. Malkowski, Center For High-Throughput Structural Biology
Date :  11 Oct 06  (Deposition) - 26 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold, Structural Genomics, Psi-2, Protein Structure Initiative, Center For High-Throughput Structural Biology, Chtsb, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. G. Malkowski, E. Quartley, A. E. Friedman, J. Babulski, Y. Kon, J. Wolfley, M. Said, J. R. Luft, E. M. Phizicky, G. T. Detitta, E. J. Grayhack
Blocking S-Adenosylmethionine Synthesis In Yeast Allows Selenomethionine Incorporation And Multiwavelength Anomalou Dispersion Phasing.
Proc. Natl. Acad. Sci. Usa V. 104 6678 2007
PubMed-ID: 17426150  |  Reference-DOI: 10.1073/PNAS.0610337104

(-) Compounds

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.2
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: BAKER'S YEAST
    Expression System Plasmid: BG2483
    Expression System Taxid: 4932
    Gene: WRS1
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: TRYPTOPHAN-TRNA LIGASE, TRPRS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1PG44Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:159 , GLY A:163 , THR A:196 , GLU A:199 , GLN A:312 , TYR A:315 , HOH A:515 , HOH A:576 , HOH A:721 , HOH A:792BINDING SITE FOR RESIDUE PG4 A 950
2AC2SOFTWARETYR A:399 , ASP A:409 , TYR A:416 , HOH A:738 , HOH A:767BINDING SITE FOR RESIDUE PG4 A 951
3AC3SOFTWAREGLN A:240 , TYR A:241 , GLY A:243 , GLY A:244 , ALA A:245 , PHE A:246 , GLU A:248 , PRO A:293 , HOH A:505 , HOH A:611BINDING SITE FOR RESIDUE PG4 A 952
4AC4SOFTWAREPHE A:411 , GLU A:414 , LYS A:418 , GLU A:423 , HOH A:713BINDING SITE FOR RESIDUE PG4 A 953

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IP1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IP1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IP1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYWC_YEAST111-121  1A:164-174

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YOL097C1YOL097C.1XV:137825-1365271299SYWC_YEAST1-4324321A:99-477 (gaps)379

(-) 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:371
 aligned with SYWC_YEAST | Q12109 from UniProtKB/Swiss-Prot  Length:432

    Alignment length:379
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415         
           SYWC_YEAST    46 DYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQGSTTKMSASDDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPK 424
               SCOP domains d2ip1a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2ip1A01 A:99-353 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                         2ip1A02 A:354-461 Tyrosyl-Transfer RNA Synthetase                                                           ---------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.ee.hhhhhhhhhhhhh...hhhhhh..eeeeehhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhh.eeeeehhhhhhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...........eeeeee..hhhhhhhhhhhhhhhh....eeeee........--------hhhhh.....hhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhh.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------AA_TRNA_LIG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:99-477 (gaps) UniProt: 1-432 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                  Transcript 1
                 2ip1 A  99 DYDKLIKQFGTKPVNEETLKRFKQVTGREPHHFLRKGLFFSERDFTKILDLYEQGKPFFLYTGRGPSSDSMHLGHMIPFVFTKWLQEVFDVPLVIELTDDEKFLFKHKLTINDVKNFARENAKDIIAVGFDPKNTFIFSDLQYMGGAFYETVVRVSRQITGSTAKAVFGFNDSDCIGKFHFASIQIATAFPSSFPNVLGLPDKTPCLIPCAIDQDPYFRVCRDVADKLKYSKPALLHSRFFPALQG--------DDTTAIFMTDTPKQIQKKINKYAFSGGQVSADLHRELGGNPDVDVAYQYLSFFKDDDVFLKECYDKYKSGELLSGEMKKLCIETLQEFVKAFQERRAQVDEETLDKFMVPHKLVWGEKERLVAPK 477
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338     |   -    |  358       368       378       388       398       408       418       428       438       448       458       468         
                                                                                                                                                                                                                                                                               344      353
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IP1)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYWC_YEAST | Q12109)
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
        SYWC_YEAST | Q12109: 3kt0 3kt3 3kt6 3kt8

(-) Related Entries Specified in the PDB File

1o5t CRYSTAL STRUCTURE OF THE AMINOACYLATION CATALYTIC FRAGMENT OF HUMAN TRYPTOPHANYL-TRNA SYNTHETASE RELATED ID: YOL097C RELATED DB: TARGETDB