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(-) Description

Title :  STRUCTURE OF TYROSYL-T/RNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RESOLUTION. INTERACTION OF THE ENZYME WITH THE TYROSYL ADENYLATE INTERMEDIATE
 
Authors :  C. Monteilhet, P. Brick, D. M. Blow
Date :  29 Jun 89  (Deposition) - 15 Oct 89  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ligase (Synthetase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Brick, T. N. Bhat, D. M. Blow
Structure Of Tyrosyl-Trna Synthetase Refined At 2. 3 A Resolution. Interaction Of The Enzyme With The Tyrosyl Adenylate Intermediate.
J. Mol. Biol. V. 208 83 1989
PubMed-ID: 2504923  |  Reference-DOI: 10.1016/0022-2836(89)90090-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TYROSYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.1
    Engineered: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1TYA1Ligand/IonPHOSPHORIC ACID 2-AMINO-3-(4-HYDROXY-PHENYL)-PROPYLESTER ADENOSIN-5'YL ESTER
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1TYA2Ligand/IonPHOSPHORIC ACID 2-AMINO-3-(4-HYDROXY-PHENYL)-PROPYLESTER ADENOSIN-5'YL ESTER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:34 , GLY A:36 , ASP A:38 , GLY A:47 , HIS A:48 , THR A:51 , LEU A:68 , THR A:73 , ASP A:78 , ASN A:123 , TYR A:169 , GLN A:173 , ASP A:176 , GLY A:191 , GLY A:192 , ASP A:194 , GLN A:195 , LEU A:222 , VAL A:223 , HOH A:423BINDING SITE FOR RESIDUE TYA A 420

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TS1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TS1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TS1)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYY_GEOSE39-49  1A:39-49
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYY_GEOSE39-49  2A:39-49

(-) Exons   (0, 0)

(no "Exon" information available for 3TS1)

(-) 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:317
 aligned with SYY_GEOSE | P00952 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:319
                                    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         
            SYY_GEOSE     1 MDLLAELQWRGLVNQTTDEDGLRKLLNEERVTLYCGFDPTADSLHIGHLATILTMRRFQQAGHRPIALVGGATGLIGDPSGKKSERTLNAKETVEAWSARIKEQLGRFLDFEADGNPAKIKNNYDWIGPLDVITFLRDVGKHFSVNYMMAKESVQSRIETGISFTEFSYMMLQAYDFLRLYETEGCRLQIGGSDQWGNITAGLELIRKTKGEARAFGLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKEEIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQAIRIS 319
               SCOP domains d3ts1a_ A: Tyrosyl-tRNA synthetase (TyrRS)                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3ts1A01 A:1-222 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                         3ts1A02 A:223-318 Tyrosyl-Transfer RNA Synthetase                                               - CATH domains
               Pfam domains -------------------------tRNA-synt_1b-3ts1A01 A:26-319                                                                                                                                                                                                                                                                          Pfam domains
         Sec.struct. author .hhhhhhhhh....ee..hhhhhhhhhh...eeeeee...........hhhhhhhhhhhh...eeeeee...hhh...............hhhhhhhhhhhhhhh.............eeee.hhhh....hhhhhhh.hhh..hhhhh..hhhh........hhhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhh.--..eeeee...........................hhhhhhhhh......hhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------AA_TRNA_LIG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ts1 A   1 MDLLAELQWRGLVNQTTDEDGLRKLLNEERVTLYCGFDPTADSLHIGHLATILTMRRFQQAGHRPIALVGGATGLIGDPSGKKSERTLNAKETVEAWSARIKEQLGRFLDFEADGNPAKIKNNYDWIGPLDVITFLRDVGKHFSVNYMMAKESVQSRIETGISFTEFSYMMLQAYDFLRLYETEGCRLQIGGSDQWGNITAGLELIRKTKG--RAFGLTIPLVTKADGTKFGKTESGTIWLDKEKTSPYEFYQFWINTDDRDVIRYLKYFTFLSKEEIEALEQELREAPEKRAAQKTLAEEVTKLVHGEEALRQAIRIS 319
                                    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         
                                                                                                                                                                                                                                            211  |                                                                                                         
                                                                                                                                                                                                                                               214
   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  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYY_GEOSE | P00952)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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: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.
    GO:0006437    tyrosyl-tRNA aminoacylation    The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-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
        SYY_GEOSE | P00952: 1jh3 1tya 1tyb 1tyc 1tyd 2ts1 4ts1

(-) Related Entries Specified in the PDB File

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