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(-) Description

Title :  STRUCTURE OF THE TYROSYL TRNA SYNTHETASE FROM ACANTHAMOEBA POLYPHAGA MIMIVIRUS COMPLEXED WITH TYROSYNOL
 
Authors :  C. Abergel, J. Rudinger-Thirion, R. Giege, J. M. Claverie
Date :  13 Sep 06  (Deposition) - 25 Sep 07  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Protein Biosynthesis, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Abergel, J. Rudinger-Thirion, R. Giege, J. M. Claverie
Virus-Encoded Aminoacyl-Trna Synthetases: Structural And Functional Characterization Of Mimivirus Tyrrs And Metrs.
J. Virol. V. 81 12406 2007
PubMed-ID: 17855524  |  Reference-DOI: 10.1128/JVI.01107-07
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PDEST17
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2-346
    Organism Scientific: ACANTHAMOEBA POLYPHAGA MIMIVIRUS
    Organism Taxid: 212035
    Synonym: TYROSINE-TRNA LIGASE, TYRRS, TYROSYL-TRNA SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1TYE2Ligand/Ion4-[(2S)-2-AMINO-3-HYDROXYPROPYL]PHENOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:34 , GLY A:36 , TYR A:161 , GLN A:165 , ASP A:168 , LEU A:182 , GLN A:186BINDING SITE FOR RESIDUE TYE A1336
2AC2SOFTWARETYR B:34 , GLY B:36 , PHE B:37 , GLN B:165 , ASP B:168BINDING SITE FOR RESIDUE TYE B1338

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J5B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J5B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J5B)

(-) Exons   (0, 0)

(no "Exon" information available for 2J5B)

(-) 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:322
 aligned with SYY_MIMIV | Q5UPJ7 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:339
                                    14        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         
            SYY_MIMIV     5 DHTNNEHRLTQLLSIAEECETLDRLKQLVDSGRIFTAYNGFEPSGRIHIAQALITVMNTNNIIECGGQMIIYIADWFAKMNLKMNGDINKIRELGRYFIEVFKACGINLDGTRFIWASEFIASNPSYIERMLDIAEFSTISRVKRCCQIMGRNESDCLKASQIFYPCMQAADVFELVPEGIDICQLGIDQRKVNMLAIEYANDRGLKIPISLSHHMLMSLSGPKKKMSKSDPQGAIFMDDTEQEVSEKISRAYCTDETFDNPIFEYIKYLLLRWFGTLNLCGKIYTDIESIQEDFSSMNKRELKTDVANYINTIIDLVREHFKKPELSELLSNVKSYQQ 343
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh...ee.hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------------.hhhhhhhhhhhhh......ee.....hhhhhhhhhhhhhhh.....eeee.................hhhhh.....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh.eee..eee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j5b A  -3 DHTNNEHRLTQLLSIAEECETLDRLKQLVDSGRIFTAYNGFEPSGRIHIAQALITVMNTNNMIECGGQMIIYIADWFAKMNLKMNGDINKIRELGRYFIEVFKACGINLDGTRFIWASEFIASNPSYIERMLDIAEFSTISRVKR-----------------IFYPCMQAADVFELVPEGIDICQLGIDQRKVNMLAIEYANDRGLKIPISLSHHMLMSLSGPKKKMSKSDPQGAIFMDDTEQEVSEKISRAYCTDETFDNPIFEYIKYLLLRWFGTLNLCGKIYTDIESIQEDFSSMNKRELKTDVANYINTIIDLVREHFKKPELSELLSNVKSYQQ 335
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136    |    -         -  |    166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326         
                                                                                                                                                                          141               159                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:321
 aligned with SYY_MIMIV | Q5UPJ7 from UniProtKB/Swiss-Prot  Length:346

    Alignment length:339
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336         
            SYY_MIMIV     7 TNNEHRLTQLLSIAEECETLDRLKQLVDSGRIFTAYNGFEPSGRIHIAQALITVMNTNNIIECGGQMIIYIADWFAKMNLKMNGDINKIRELGRYFIEVFKACGINLDGTRFIWASEFIASNPSYIERMLDIAEFSTISRVKRCCQIMGRNESDCLKASQIFYPCMQAADVFELVPEGIDICQLGIDQRKVNMLAIEYANDRGLKIPISLSHHMLMSLSGPKKKMSKSDPQGAIFMDDTEQEVSEKISRAYCTDETFDNPIFEYIKYLLLRWFGTLNLCGKIYTDIESIQEDFSSMNKRELKTDVANYINTIIDLVREHFKKPELSELLSNVKSYQQPS 345
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..ee.hhhhhhhhhhhh..eeeeeee......hhhhhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.------------------.hhhhhhhhhhhhh......ee.....hhhhhhhhhhhhhhh.....eeee................hhhhhh.....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh.eee..eee.hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j5b B  -1 TNNEHRLTQLLSIAEECETLDRLKQLVDSGRIFTAYNGFEPSGRIHIAQALITVMNTNNMIECGGQMIIYIADWFAKMNLKMNGDINKIRELGRYFIEVFKACGINLDGTRFIWASEFIASNPSYIERMLDIAEFSTISRVK------------------IFYPCMQAADVFELVPEGIDICQLGIDQRKVNMLAIEYANDRGLKIPISLSHHMLMSLSGPKKKMSKSDPQGAIFMDDTEQEVSEKISRAYCTDETFDNPIFEYIKYLLLRWFGTLNLCGKIYTDIESIQEDFSSMNKRELKTDVANYINTIIDLVREHFKKPELSELLSNVKSYQQPS 337
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138 |       -         -|      168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328         
                                                                                                                                                                       140                159
   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  (0, 0)

(no "SCOP Domain" information available for 2J5B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J5B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J5B)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYY_MIMIV | Q5UPJ7)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0004831    tyrosine-tRNA ligase activity    Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H(+).
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.

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