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(-) Description

Title :  METHIONYL-TRNA SYNTHETASE FROM PYROCOCCUS ABYSSI
 
Authors :  T. Crepin, E. Schmitt, S. Blanquet, Y. Mechulam
Date :  05 Dec 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Translation, Dimerization, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Crepin, E. Schmitt, S. Blanquet, Y. Mechulam
Three-Dimensional Structure Of Methionyl-Trna Synthetase From Pyrococcus Abyssi.
Biochemistry V. 43 2635 2004
PubMed-ID: 14992601  |  Reference-DOI: 10.1021/BI0356247
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHIONYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3AMETPA-SD
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: METG, METS, PYRAB09870, PAB2364
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292
    Synonym: METHIONINE--TRNA LIGASE, METRS

 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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:127 , ASP A:130 , CYS A:173 , CYS A:176BINDING SITE FOR RESIDUE ZN A 801
2AC2SOFTWARECYS A:143 , CYS A:146 , CYS A:156 , VAL A:158 , CYS A:159BINDING SITE FOR RESIDUE ZN A 802

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYM_PYRAB11-22  1A:11-22
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYM_PYRAB11-22  2A:11-22

(-) Exons   (0, 0)

(no "Exon" information available for 1RQG)

(-) 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:606
 aligned with SYM_PYRAB | Q9V011 from UniProtKB/Swiss-Prot  Length:722

    Alignment length:606
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600      
            SYM_PYRAB     1 MVRYMVTSALPYANGPIHAGHLAGAYLPADIFVRYLRLKGEDVVFICGTDEHGTPISFRALKEGRSPREIVDEFHEQIKITFQRAKISFDFFGRTELPIHYKLSQEFFLKAYENGHLVKKVTKQAYCEHDKMFLPDRFVIGTCPYCGAEDQKGDQCEVCGRPLTPEILINPRCAICGRPISFRDSAHYYIKMQDFAERLKRWIEKQPWKPNVKNMVLSWIEEGLEERAITRDLNWGIPVPLDEEDMKGKVLYVWFEAPIGYISITIEHFKRIGKPNEWKKYWLNIDGQTRVIHFIGKDNIPFHAIFWPAFLMAYGKYKDEEVEAEWNLPYDIPANEYLTLEGKKFSTSRNWAIWVHEFLDVFPADYLRYYLTTIMPETRDSDFSFSDFKVRINEELVNNLGNFVHRALTFVNRYFDGVVPERGELDELDREALEEIEKAFKEVGELIMNYRFKDALKRVMSLASFGNRYFDHKQPWKTAKEDKVRTGTTVNISLQIVKALGILLEPFLPDASEKIWHLLNLDEVKRWEFRELPAGHKVRKPEILFKKVTDDQIIYFILNYMAKGNPEGARILLDKYYKREDVIRVAKEKFGDEAEVVLRRVYKDIK 606
               SCOP domains d1rqga2 A:1-138,A:174-396 Methionyl-tRNA synthetase (MetRS)                                                                               d1rqga3 A:139-173                  d1rqga2 A:1-138,A:174-396 Methionyl-tRNA synthetase (MetRS)                                                                                                                                                                    d1rqga1 A:397-606 Methionyl-tRNA synthetase (MetRS)                                                                                                                                                                SCOP domains
               CATH domains 1rqgA01 A:1-97,A:252-336 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                   1rqgA02 A:98-251  [code=2.170.220.10, no name defined]                                                                                                    1rqgA01 A:1-97,A:252-336 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1       ------------------------------------------------------------1rqgA04 A:397-547 Isoleucyl-tRNA Synthetase; Domain 1                                                                                                  ----------------------------------------------------------- CATH domains
               Pfam domains ---tRNA-synt_1g-1rqgA01 A:4-408                                                                                                                                                                                                                                                                                                                                                                                         --------------------Anticodon_1-1rqgA02 A:429-552                                                                                               ------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhh..eeeeeeeeee........hhhhh.........................................eeeeeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhh.....ee.ee..................eehhhhhh.hhhhhhhhhhhhhh.....hhhhhh.....eeeeeeee..hhhhhhhhhhhhhhh....................ee..eee..ee.........hhhhhh...hhhhhhhhhhhh......eeehhhhhhhhhhhh...hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.............................hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------AA_TRNA_LIGA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1rqg A   1 MVRYMVTSALPYANGPIHAGHLAGAYLPADIFVRYLRLKGEDVVFICGTDEHGTPISFRALKEGRSPREIVDEFHEQIKITFQRAKISFDFFGRTELPIHYKLSQEFFLKAYENGHLVKKVTKQAYCEHDKMFLPDRFVIGTCPYCGAEDQKGDQCEVCGRPLTPEILINPRCAICGRPISFRDSAHYYIKMQDFAERLKRWIEKQPWKPNVKNMVLSWIEEGLEERAITRDLNWGIPVPLDEEDMKGKVLYVWFEAPIGYISITIEHFKRIGKPNEWKKYWLNIDGQTRVIHFIGKDNIPFHAIFWPAFLMAYGKYKDEEVEAEWNLPYDIPANEYLTLEGKKFSTSRNWAIWVHEFLDVFPADYLRYYLTTIMPETRDSDFSFSDFKVRINEELVNNLGNFVHRALTFVNRYFDGVVPERGELDELDREALEEIEKAFKEVGELIMNYRFKDALKRVMSLASFGNRYFDHKQPWKTAKEDKVRTGTTVNISLQIVKALGILLEPFLPDASEKIWHLLNLDEVKRWEFRELPAGHKVRKPEILFKKVTDDQIIYFILNYMAKGNPEGARILLDKYYKREDVIRVAKEKFGDEAEVVLRRVYKDIK 606
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600
   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 Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HUP (230)
(-)
Clan: no clan defined [family: Anticodon_1] (10)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYM_PYRAB | Q9V011)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004825    methionine-tRNA ligase activity    Catalysis of the reaction: ATP + L-methionine + tRNA(Met) = AMP + diphosphate + L-methionyl-tRNA(Met).
    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:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
biological process
    GO:0006431    methionyl-tRNA aminoacylation    The process of coupling methionine to methionyl-tRNA, catalyzed by methionyl-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: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.

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        SYM_PYRAB | Q9V011: 1mkh

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