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(-) Description

Title :  GLUTAMYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS IN COMPLEX WITH L-GLUTAMATE
 
Authors :  S. Sekine, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  31 May 05  (Deposition) - 05 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sekine, M. Shichiri, S. Bernier, R. Chenevert, J. Lapointe, S. Yokoyama
Structural Bases Of Transfer Rna-Dependent Amino Acid Recognition And Activation By Glutamyl-Trna Synthetase
Structure V. 14 1791 2006
PubMed-ID: 17161369  |  Reference-DOI: 10.1016/J.STR.2006.10.005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PK7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: GLUTAMATE--TRNA LIGASE, GLURS

 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
1GLU1Mod. Amino AcidGLUTAMIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:5 , ALA A:7 , SER A:9 , GLU A:41 , TYR A:187 , ARG A:205 , TRP A:209 , HOH A:1024BINDING SITE FOR RESIDUE GLU A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:78 -Pro A:79
2Arg A:152 -Pro A:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYE_THET88-19  1A:8-19

(-) Exons   (0, 0)

(no "Exon" information available for 2CUZ)

(-) 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:469
 aligned with SYE_THET8 | P27000 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             468 
                                    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       | 
            SYE_THET8     1 MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARYVPGAEERILAALKWLGLSYDEGPDVGGPHGPYRQSERLPLYQKYAEELLKRGWAYRAFETPEELEQIRKEKGGYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKDELRGVVVYDNQEIPDVVLLKSDGYPTYHLANVVDDHLMGVTDVIRAEEWLVSTPIHVLLYRAFGWEAPRFYHMPLLRNPDKTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTWERVSLGGPVFDLEKLRWMNGKYIREVLSLEEVAERVKPFLREAGLSWESEAYLRRAVELMRPRFDTLKEFPEKARYLFTEDYPVSEKAQRKLEEGLPLLKELYPRLRAQEEWTEAALEALLRGFAAEKGVKLGQVAQPLRAALTGSLETPGLFEILALLGKERALRRLERALA-   -
               SCOP domains d2cuza2 A:1-305 Glutamyl-tRNA synthetase (GluRS)                                                                                                                                                                                                                                                                 d2cuza1 A:306-468 C-terminal domain of glutamyl-tRNA synthetase (GluRS)                                                                                            - SCOP domains
               CATH domains 2cuzA01 A:1-70,A:187-237                                              2cuzA02 A:71-186 Glutamyl-tRNA Synthetase; Domain 3                                                                 2cuzA01 A:1-70,A:187-237                           2cuzA03 A:238-322 Glutamyl-trna Synthetase; Domain 2                                 2cuzA04 A:323-370                               2cuzA05 A:371-468  [code=1.10.10.350, no name defined]                                            - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........hhhhhhhhhhhhhhhhhh..eeee............hhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeee......eeeeee...eeeeee.hhh...eee......hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhh..hhhhhhhhhhh............hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------AA_TRNA_LIGA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cuz A   1 MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARYVPGAEERILAALKWLGLSYDEGPDVGGPHGPYRQSERLPLYQKYAEELLKRGWAYRAFETPEELEQIRKEKGGYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKDELRGVVVYDNQEIPDVVLLKSDGYPTYHLANVVDDHLMGVTDVIRAEEWLVSTPIHVLLYRAFGWEAPRFYHMPLLRNPDKTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTWERVSLGGPVFDLEKLRWMNGKYIREVLSLEEVAERVKPFLREAGLSWESEAYLRRAVELMRPRFDTLKEFPEKARYLFTEDYPVSEKAQRKLEEGLPLLKELYPRLRAQEEWTEAALEALLRGFAAEKGVKLGQVAQPLRAALTGSLETPGLFEILALLGKERALRRLERALAE 501
                                    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       ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             468|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              501
   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  (2, 2)

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

(-) CATH Domains  (5, 5)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYE_THET8 | P27000)
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:0004818    glutamate-tRNA ligase activity    Catalysis of the reaction: ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu).
    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:0016876    ligase activity, forming aminoacyl-tRNA and related compounds    Catalysis of the joining of an amino acid and a nucleic acid (usually tRNA) or poly(ribitol phosphate), with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. The reaction forms an aminoacyl-tRNA or a related compound.
    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:0006424    glutamyl-tRNA aminoacylation    The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-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:0043039    tRNA aminoacylation    The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        SYE_THET8 | P27000: 1g59 1gln 1j09 1n75 1n77 1n78 2cv0 2cv1 2cv2 2dxi

(-) Related Entries Specified in the PDB File

1g59
1gln
1j09
1n75
1n77
1n78
2cv0 THE SAME PROTEIN COMPLEXED WITH TRNA(GLU), L-GLUTAMATE
2cv1 THE SAME PROTEIN COMPLEXED WITH TRNA(GLU), ATP, AN ANALOG OF L-GLUTAMATE: A QUATERNARY COMPLEX
2cv2 THE SAME PROTEIN COMPLEXED WITH TRNA(GLU), AN ENZYME INHIBITOR, GLU-AMS
2dxi RELATED ID: TTK003000897.9 RELATED DB: TARGETDB