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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS
 
Authors :  T. Yanagisawa, T. Sumida, R. Ishii, S. Sekine, S. Yokoyama, Riken Stru Genomics/Proteomics Initiative (Rsgi)
Date :  26 Mar 07  (Deposition) - 18 Mar 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trna, Aminoacyl-Trna Synthetase, Translation, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yanagisawa, T. Sumida, R. Ishii, K. Sakamoto, M. Shirouzu, S. Sekine, A. Shinkai, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Tryptophanyl-Trna Synthetase From Thermus Thermophilus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TRPS
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:105 , GLU A:160BINDING SITE FOR RESIDUE PO4 A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EL7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2EL7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EL7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2EL7)

(-) Exons   (0, 0)

(no "Exon" information available for 2EL7)

(-) 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:318
 aligned with Q5SIY7_THET8 | Q5SIY7 from UniProtKB/TrEMBL  Length:337

    Alignment length:331
                                    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       330 
         Q5SIY7_THET8     1 MKRVLSGIQPSGEIHIGNYLGAIKQWVAIGEKLGRDAFFCIVDYHALTNPLAYDPSTLAQRTFEAALVNIAAGLDPEKVTLFVQSHVPEHTELSWVFTTLTPLGDLTRMTQFKDKASKQETVWSGLLMYPVLQAADILIYKADTVPVGEDQVQHIELTREIARRFNHLFGETFPEPQALLNPEAPRVPGIDGKAKMSKSLGNTIGLLEPEESIWQKIQHLPDDPQRIRLSDPGDPERTILFTYLSYFAPKDLVEALKEEYRKAGVGTYVVKRILFDHLMEALRPIRERAEALKKDPDYVMDALLEGAKRARAVAQATMEEVREKVGLLLPR 331
               SCOP domains d2el7a_ A: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2el7A02 A:189-295 Tyrosyl-Transfer R             NA Synthetase                                             ------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhh....hhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhh......eee.............................hhhhhhhhhhh.....-------------hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2el7 A   1 MKRVLSGIQPSGEIHIGNYLGAIKQWVAIGEKLGRDAFFCIVDYHALTNPLAYDPSTLAQRTFEAALVNIAAGLDPEKVTLFVQSHVPEHTELSWVFTTLTPLGDLTRMTQFKDKASKQETVWSGLLMYPVLQAADILIYKADTVPVGEDQVQHIELTREIARRFNHLFGETFPEPQALLNPEAPRVPGIDGKAKMSKSLGNTIGLLEPEESIWQKIQHLPDDP-------------TILFTYLSYFAPKDLVEALKEEYRKAGVGTYVVKRILFDHLMEALRPIRERAEALKKDPDYVMDALLEGAKRARAVAQATMEEVREKVGLLLPR 331
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   |     -       240       250       260       270       280       290       300       310       320       330 
                                                                                                                                                                                                                                                         224           238                                                                                             


Chain B from PDB  Type:PROTEIN  Length:316
 aligned with Q5SIY7_THET8 | Q5SIY7 from UniProtKB/TrEMBL  Length:337

    Alignment length:330
                                    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       330
         Q5SIY7_THET8     1 MKRVLSGIQPSGEIHIGNYLGAIKQWVAIGEKLGRDAFFCIVDYHALTNPLAYDPSTLAQRTFEAALVNIAAGLDPEKVTLFVQSHVPEHTELSWVFTTLTPLGDLTRMTQFKDKASKQETVWSGLLMYPVLQAADILIYKADTVPVGEDQVQHIELTREIARRFNHLFGETFPEPQALLNPEAPRVPGIDGKAKMSKSLGNTIGLLEPEESIWQKIQHLPDDPQRIRLSDPGDPERTILFTYLSYFAPKDLVEALKEEYRKAGVGTYVVKRILFDHLMEALRPIRERAEALKKDPDYVMDALLEGAKRARAVAQATMEEVREKVGLLLP 330
               SCOP domains d2el7b_ B: Tryptophanyl-tRNA synthetase (TrpRS)                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2el7B02 B:189-295 Tyrosyl-Transfer               RNA Synthetase                                            ----------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhh.......hhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhhhhh......eee.............................hhhhhhhhhhh....--------------hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2el7 B   1 MKRVLSGIQPSGEIHIGNYLGAIKQWVAIGEKLGRDAFFCIVDYHALTNPLAYDPSTLAQRTFEAALVNIAAGLDPEKVTLFVQSHVPEHTELSWVFTTLTPLGDLTRMTQFKDKASKQETVWSGLLMYPVLQAADILIYKADTVPVGEDQVQHIELTREIARRFNHLFGETFPEPQALLNPEAPRVPGIDGKAKMSKSLGNTIGLLEPEESIWQKIQHLPDD--------------TILFTYLSYFAPKDLVEALKEEYRKAGVGTYVVKRILFDHLMEALRPIRERAEALKKDPDYVMDALLEGAKRARAVAQATMEEVREKVGLLLP 330
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  |      -       240       250       260       270       280       290       300       310       320       330
                                                                                                                                                                                                                                                        223            238
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EL7)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5SIY7_THET8 | Q5SIY7)
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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