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(-) Description

Title :  METHIONYL-TRNA SYNTHETASE ZINC BINDING DOMAIN. 3D STRUCTURE AND HOMOLOGY WITH RUBREDOXIN AND GAG RETROVIRAL PROTEINS
 
Authors :  D. Fourmy, F. Dardel
Date :  09 Nov 92  (Deposition) - 31 Oct 93  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Aminoacyl-Trna Synthase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Fourmy, F. Dardel, S. Blanquet
Methionyl-Trna Synthetase Zinc Binding Domain. Three-Dimensional Structure And Homology With Rubredoxin And Gag Retroviral Proteins.
J. Mol. Biol. V. 231 1078 1993
PubMed-ID: 8515466  |  Reference-DOI: 10.1006/JMBI.1993.1353
(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 Gene: GAG
    Gene: GAG
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  
NMR Structure : 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:10 , CYS A:13 , CYS A:23 , CYS A:26BINDING SITE FOR RESIDUE ZN A 29
2ZNCUNKNOWNCYS A:10 , CYS A:13 , CYS A:23 , CYS A:26NULL

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MEA)

(-) Exons   (0, 0)

(no "Exon" information available for 1MEA)

(-) Sequences/Alignments

NMR Structure
   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:28
 aligned with SYM_ECOLI | P00959 from UniProtKB/Swiss-Prot  Length:677

    Alignment length:31
                                   143       153       163 
            SYM_ECOLI   134 GMFLPDRFVKGTCPKCKSPDQYGDNCEVCGA 164
               SCOP domains d   1meaa_ A:                   SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains -----tRNA-synt_1g-1meaA01       Pfam domains
         Sec.struct. author .---........................... Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 1mea A   1 G---SDRFVKGTCPKCKSPDQYGDNCEVCGA  28
                            |   |    7        17        27 
                            |   2                          
                            1
   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)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1MEA)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HUP (230)

(-) Gene Ontology  (16, 16)

NMR Structure(hide GO term definitions)
Chain A   (SYM_ECOLI | P00959)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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UniProtKB/Swiss-Prot
        SYM_ECOLI | P00959: 1f4l 1med 1p7p 1pfu 1pfv 1pfw 1pfy 1pg0 1pg2 1qqt 3h97 3h99 3h9b 3h9c

(-) Related Entries Specified in the PDB File

1med