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(-) Description

Title :  YEAST ARGINYL-TRNA SYNTHETASE
 
Authors :  J. Cavarelli, B. Delagouute, G. Eriani, J. Gangloff, D. Moras
Date :  31 Aug 98  (Deposition) - 27 Aug 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Aminoacyl-Trna Synthetase, Protein Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Cavarelli, B. Delagoutte, G. Eriani, J. Gangloff, D. Moras
L-Arginine Recognition By Yeast Arginyl-Trna Synthetase.
Embo J. V. 17 5438 1998
PubMed-ID: 9736621  |  Reference-DOI: 10.1093/EMBOJ/17.18.5438
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ARGINYL-TRNA SYNTHETASE)
    Atcc: YDR341C S70106
    Cellular Location: CYTOPLASM
    Chains: A
    Collection: YDR341C S70106
    EC Number: 6.1.1.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: YEAST GENOME, CHROMOSOME IV, OPEN READING FRAME YDR341C, ACCESSION NUMBER S70106
    Synonym: ARGRS, ARGININE - TRNA LIGASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ARG1Mod. Amino AcidARGININE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:79 , GLU A:148 , SER A:151 , ASN A:153 , HIS A:162 , TYR A:188 , TYR A:347 , ASP A:351 , TYR A:369 , GLN A:375BINDING SITE FOR RESIDUE ARG A 900

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BS2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1BS2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1BS2)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYRC_YEAST152-163  1A:152-163

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR341C1YDR341C.1IV:1153621-11517981824SYRC_YEAST1-6076071A:5-607603

(-) 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:604
 aligned with SYRC_YEAST | Q05506 from UniProtKB/Swiss-Prot  Length:607

    Alignment length:604
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    607 
                                    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       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604  | 
           SYRC_YEAST     5 ANMISQLKKLSIAEPAVAKDSHPDVNIVDLMRNYISQELSKISGVDSSLIFPALEWTNTMERGDLLIPIPRLRIKGANPKDLAVQWAEKFPCGDFLEKVEANGPFIQFFFNPQFLAKLVIPDILTRKEDYGSCKLVENKKVIIEFSSPNIAKPFHAGHLRSTIIGGFLANLYEKLGWEVIRMNYLGDWGKQFGLLAVGFERYGNEEALVKDPIHHLFDVYVRINKDIEEEGDSIPLEQSTNGKAREYFKRMEDGDEEALKIWKRFREFSIEKYIDTYARLNIKYDVYSGESQVSKESMLKAIDLFKEKGLTHEDKGAVLIDLTKFNKKLGKAIVQKSDGTTLYLTRDVGAAMDRYEKYHFDKMIYVIASQQDLHAAQFFEILKQMGFEWAKDLQHVNFGMVQGMSTRKGTVVFLDNILEETKEKMHEVMKKNENKYAQIEHPEEVADLVGISAVMIQDMQGKRINNYEFKWERMLSFEGDTGPYLQYAHSRLRSVERNASGITQEKWINADFSLLKEPAAKLLIRLLGQYPDVLRNAIKTHEPTTVVTYLFKLTHQVSSCYDVLWVAGQTEELATARLALYGAARQVLYNGMRLLGLTPVERM-   -
               SCOP domains d1bs2a3 A:5-135 Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain                                                    d1bs2a2 A:136-483 Arginyl-tRNA synthetase (ArgRS)                                                                                                                                                                                                                                                                                                           d1bs2a1 A:484-607 Arginyl-tRNA synthetase (ArgRS)                                                                           - SCOP domains
               CATH domains 1bs2A03 A:5-135  [code=3.30.1360.70, no name defined]                                                                              1bs2A01 A:136-482 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                                                                                    1bs2A02 A:483-607 Isoleucyl-tRNA Synthetase; Domain 1                                                                        - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.................hhhhhhhhhhhhhhhh....hhhhhhheee...hhh..eeeehhhh......hhhhhhhhhhh......eeeeeee..eeeeee.hhhhhhhhhhhhhhhhhh..........eeeee...........hhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhh..hhhhhh.hhhhhhhhhhhhhhhhhh..........hhhhhhhhh.............hhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhh.........eeeehhh......eeeee.......hhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...hhhhheeee..................hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...........hhhhh......hhhhhhhhhhhhhhh......hhhhhh...hhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------AA_TRNA_LIGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:5-607 UniProt: 1-607 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         - Transcript 1
                 1bs2 A   5 ANMISQLKKLSIAEPAVAKDSHPDVNIVDLMRNYISQELSKISGVDSSLIFPALEWTNTMERGDLLIPIPRLRIKGANPKDLAVQWAEKFPCGDFLEKVEANGPFIQFFFNPQFLAKLVIPDILTRKEDYGSCKLVENKKVIIEFSSPNIAKPFHAGHLRSTIIGGFLANLYEKLGWEVIRMNYLGDWGKQFGLLAVGFERYGNEEALVKDPIHHLFDVYVRINKDIEEEGDSIPLEQSTNGKAREYFKRMEDGDEEALKIWKRFREFSIEKYIDTYARLNIKYDVYSGESQVSKESMLKAIDLFKEKGLTHEDKGAVLIDLTKFNKKLGKAIVQKSDGTTLYLTRDVGAAMDRYEKYHFDKMIYVIASQQDLHAAQFFEILKQMGFEWAKDLQHVNFGMVQGMSTRKGTVVFLDNILEETKEKMHEVMKKNENKYAQIEHPEEVADLVGISAVMIQDMQGKRINNYEFKWERMLSFEGDTGPYLQYAHSRLRSVERNASGITQEKWINADFSLLKEPAAKLLIRLLGQYPDVLRNAIKTHEPTTVVTYLFKLTHQVSSCYDVLWVAGQTEELATARLALYGAARQVLYNGMRLLGLTPVERMR 900
                                    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       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604  ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    607|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     900
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BS2)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYRC_YEAST | Q05506)
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:0004814    arginine-tRNA ligase activity    Catalysis of the reaction: ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg).
    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.
biological process
    GO:0006420    arginyl-tRNA aminoacylation    The process of coupling arginine to arginyl-tRNA, catalyzed by arginyl-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.
    GO:0032543    mitochondrial translation    The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SYRC_YEAST | Q05506: 1f7u 1f7v

(-) Related Entries Specified in the PDB File

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