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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUTAMYL-TRNA SYNTHETASE 1 (EC 6.1.1.17) (GLUTAMATE-TRNA LIGASE 1) (GLURS 1) (TM1351) FROM THERMOTOGA MARITIMA AT 2.5 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  06 Dec 06  (Deposition) - 19 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym./Biol. Unit :  A
Keywords :  Tm1351, Glutamyl-Trna Synthetase 1, Ec 6. 1. 1. 17, Glutamate-Trna Ligase 1, Glurs 1, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Glutamyl-Trna Synthetase 1 (Ec 6. 1. 1. 17) (Glutamate-Trna Ligase 1) (Glurs 1) (Tm1351) From Thermotoga Maritima At 2. 5 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTAMYL-TRNA SYNTHETASE 1
    Chains: A
    EC Number: 6.1.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GLTX1
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: GLUTAMATE-TRNA LIGASE 1, GLURS 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:5 , TYR A:194 , ARG A:212BINDING SITE FOR RESIDUE CL A 470
2AC2SOFTWAREARG A:435BINDING SITE FOR RESIDUE CL A 472
3AC3SOFTWAREVAL A:168 , VAL A:169 , ASP A:303 , LEU A:305BINDING SITE FOR RESIDUE GOL A 473

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O5R)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:78 -Pro A:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O5R)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYE1_THEMA8-19  1A:8-19

(-) Exons   (0, 0)

(no "Exon" information available for 2O5R)

(-) 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:468
 aligned with SYE1_THEMA | Q9X172 from UniProtKB/Swiss-Prot  Length:469

    Alignment length: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        
           SYE1_THEMA     1 MVRVRFAPSPTGFLHVGGARTALFNFLFARKEKGKFILRIEDTDLERSEREYEEKLMESLRWLGLLWDEGPDVGGDHGPYRQSERVEIYREHAERLVKEGKAYYVYAYPEEIEEMREKLLSEGKAPHYSQEMFEKFDTPERRREYEEKGLRPAVFFKMPRKDYVLNDVVKGEVVFKTGAIGDFVIMRSNGLPTYNFACVVDDMLMEITHVIRGDDHLSNTLRQLALYEAFEKAPPVFAHVSTILGPDGKKLSKRHGATSVEAFRDMGYLPEALVNYLALLGWSHPEGKELLTLEELISSFSLDRLSPNPAIFDPQKLKWMNGYYLRNMPIEKLAELAKPFFEKAGIKIIDEEYFKKVLEITKERVEVLSEFPEESRFFFEDPAPVEIPEEMKEVFSQLKEELQNVRWTMEEITPVFKKVLKQHGVKPKEFYMTLRRVLTGREEGPELVNIIPLLGKEIFLRRIERSLG 468
               SCOP domains d2o5ra1 A:1-312 automated matches                                                                                                                                                                                                                                                                                       d2o5ra2 A:313-468 automated matches                                                                                                                          SCOP domains
               CATH domains -2o5rA01 A:2-70,A:194-244                                             2o5rA02 A:71-193 Glutamyl-tRNA Synthetase; Domain 3                                                                        2o5rA01 A:2-70,A:194-244                           2o5rA03 A:245-327 Glutamyl-trna Synthetase; Domain 2                               -2o5rA04 A:329-376                               2o5rA05 A:377-468  [code=1.10.10.350, no name defined]                                       CATH domains
               Pfam domains tRNA-synt_1c-2o5rA01 A:1-319                                                                                                                                                                                                                                                                                                   ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........hhhhhhhhhhhhhhhhhhh.eeee........hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhh..eeee......hhhhhhhhhhh......hhhhhh...hhhhhhhhhhh....eeee......eeeee...eeeee.......eeee......hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.....eeeee..ee.......hhhhh..hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhh........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------AA_TRNA_LIGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o5r A   1 mVRVRFAPSPTGFLHVGGARTALFNFLFARKEKGKFILRIEDTDLERSEREYEEKLmESLRWLGLLWDEGPDVGGDHGPYRQSERVEIYREHAERLVKEGKAYYVYAYPEEIEEmREKLLSEGKAPHYSQEmFEKFDTPERRREYEEKGLRPAVFFKmPRKDYVLNDVVKGEVVFKTGAIGDFVImRSNGLPTYNFACVVDDmLmEITHVIRGDDHLSNTLRQLALYEAFEKAPPVFAHVSTILGPDGKKLSKRHGATSVEAFRDmGYLPEALVNYLALLGWSHPEGKELLTLEELISSFSLDRLSPNPAIFDPQKLKWmNGYYLRNmPIEKLAELAKPFFEKAGIKIIDEEYFKKVLEITKERVEVLSEFPEESRFFFEDPAPVEIPEEmKEVFSQLKEELQNVRWTmEEITPVFKKVLKQHGVKPKEFYmTLRRVLTGREEGPELVNIIPLLGKEIFLRRIERSLG 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        
                            |                                                      57-MSE                                                   115-MSE          132-MSE                   158-MSE                     186-MSE          203-MSE                                                        266-MSE                                               320-MSE 328-MSE                                                        391-MSE           409-MSE                432-MSE                                
                            1-MSE                                                                                                                                                                                                     205-MSE
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SYE1_THEMA | Q9X172)
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: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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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