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(-) Description

Title :  GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH ATP
 
Authors :  J. G. Arnez, D. Moras
Date :  27 Jan 99  (Deposition) - 28 Jan 99  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoacyl-Trna Synthase, Ligase(Synthetase), Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. G. Arnez, A. C. Dock-Bregeon, D. Moras
Glycyl-Trna Synthetase Uses A Negatively Charged Pit For Specific Recognition And Activation Of Glycine.
J. Mol. Biol. V. 286 1449 1999
PubMed-ID: 10064708  |  Reference-DOI: 10.1006/JMBI.1999.2562
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCINE--TRNA LIGASE
    Chains: A, B
    EC Number: 6.1.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: GLYS
    Expression System Plasmid: PGRS
    Expression System Strain: BL21 (DE3) PLYS
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Expression System Vector Type: PLASMID
    Gene: GLYQS, GLYS, TTHA0543
    Organism Scientific: THERMUS THERMOPHILUS (STRAIN HB8 / ATCC 27634 / DSM 579)
    Organism Taxid: 300852
    Other Details: ATP BOUND IN ACTIVE SITE OF EACH MONOMER
    Strain: HB8 / ATCC 27634 / DSM 579
    Synonym: GLYCYL-TRNA SYNTHETASE,GLYRS,GLYCYL-TRNA SYNTHETASE,GLYRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:220 , GLU A:222 , PHE A:230 , ARG A:231 , VAL A:232 , PHE A:235 , GLU A:304 , LEU A:305 , SER A:361 , GLY A:363 , ARG A:366 , HOH A:551BINDING SITE FOR RESIDUE ATP A 1552
2AC2SOFTWAREARG B:220 , PHE B:230 , ARG B:231 , VAL B:232 , PHE B:235 , GLN B:237 , GLU B:304 , LEU B:305 , GLU B:306 , SER B:361 , GLY B:363 , ARG B:366 , HOH B:553BINDING SITE FOR RESIDUE ATP B 2552
3S1AAUTHORGLU A:188 , ARG A:220 , GLU A:222 , ARG A:231 , VAL A:232 , PHE A:235 , GLN A:237 , GLU A:239 , GLU A:241 , ASP A:293 , GLU A:304 , ARG A:311 , ASP A:315 , GLU A:359 , SER A:361 , ARG A:366 , ATP A:1552GLYCINE AND ATP BINDING SITE, WITH ATP BOUND.
4S1BAUTHORGLU B:188 , ARG B:220 , GLU B:222 , ARG B:231 , VAL B:232 , PHE B:235 , GLN B:237 , GLU B:239 , GLU B:241 , ASP B:293 , GLU B:304 , ARG B:311 , ASP B:315 , GLU B:359 , SER B:361 , ARG B:366 , ATP B:2552GLYCINE AND ATP BINDING SITE, WITH ATP BOUND.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B76)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B76)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B76)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B76)

(-) Exons   (0, 0)

(no "Exon" information available for 1B76)

(-) 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:442
 aligned with SYG_THET8 | P56206 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:505
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501     
            SYG_THET8     2 PASSLDELVALCKRRGFIFQSSEIYGGLQGVYDYGPLGVELKNNLKQAWWRRNVYERDDMEGLDASVLTHRLVLHYSGHEATFADPMVDNRITKKRYRLDHLLKEQPEEVLKRLYRAMEVEEENLHALVQAMMQAPERAGGAMTAAGVLDPASGEPGDWTPPRYFNMMFKTYVGPVEDEASLAYLRPETAQGIFVNFKNVLDATSRKLPFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGEDEYWHRYWVEERLKWWQEMGLSRENLVPYQQPPEELAHYAKATVDILYRFPHGLEELEGIANRTDFDLGSHTKDQEALGITARVLRNEHSTQRLAYRDPETGKWFVPYVIEPSAGVDRGVLALLAEAFTREELPNGEERIVLKLKPQLAPIKVAVIPLVKNRPEITEYAKRLKARLLALGLGRVLYEDTGNIGKAYRRHDEVGTPFAVTVDYDTIGQSKDGTTRLKDTVTVRDRDTMEQIRLHVDELEGFLRERLRW 506
               SCOP domains d1b76a2 A:1-394 Glycyl-tRNA synthetase (GlyRS)                                                                                                                                                                                                                                                                                                                                                            d1b76a1 A:395-505 Glycyl-tRNA synthetase (GlyRS), C-terminal domain                                             SCOP domains
               CATH domains 1b76A01 A:1-374 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                                                   ------------------1b76A02 A:393-505  [code=3.40.50.800, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...eee..hhh......eee.hhhhhhhhhhhhhhhhhh......eeee....eeehhhhhh..hhhh.eeee...--.....-------------------------------------------------------------....eeee..eeee......hhheeee...hhhhhhhhhhhhhhhh.....eeeeeeeeee..............eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh....hhheeeee............eeeeeeee..eeeeeeeee....hhhhh.....................................eeeeeeeehhhhhhhhhhhheeee.......eeee...hhh....eeeee.....hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhh....eeeee.hhhh............eeeeee.....eeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b76 A   1 AASSLDELVALCKRRGFIFQSSEIYGGLQGVYDYGPLGVELKNNLKQAWWRRNVYERDDMEGLDASVLTHRLVLHYSGHEATFADPMVDN--AKARY-------------------------------------------------------------WTPPRYFNMMFQDLRGPRGGRGLLAYLRPETAQGIFVNFKNVLDATSRKLGFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGEDEYWHRYWVEERLKWWQEMGLSRENLVPYQQPPESSAHYAKATVDILYRFPHGSLELEGIAQRTDFDLGSHTKDQEALGITARVLRNEHSTQRLAYRDPETGKWFVPYVIEPSAGVDRGVLALLAEAFTREELPNGEERIVLKLKPQLAPIKVAVIPLVKNRPEITEYAKRLKARLLALGLGRVLYEDTGNIGKAYRRHDEVGTPFAVTVDYDTIGQSKDGTTRLKDTVTVRDRDTMEQIRLHVDELEGFLRERLRW 505
                                    10        20        30        40        50        60        70        80        90  |   |  -         -         -         -         -         -       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     
                                                                                                                    90 91  95                                                           159                                                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:442
 aligned with SYG_THET8 | P56206 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:505
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501     
            SYG_THET8     2 PASSLDELVALCKRRGFIFQSSEIYGGLQGVYDYGPLGVELKNNLKQAWWRRNVYERDDMEGLDASVLTHRLVLHYSGHEATFADPMVDNRITKKRYRLDHLLKEQPEEVLKRLYRAMEVEEENLHALVQAMMQAPERAGGAMTAAGVLDPASGEPGDWTPPRYFNMMFKTYVGPVEDEASLAYLRPETAQGIFVNFKNVLDATSRKLPFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGEDEYWHRYWVEERLKWWQEMGLSRENLVPYQQPPEELAHYAKATVDILYRFPHGLEELEGIANRTDFDLGSHTKDQEALGITARVLRNEHSTQRLAYRDPETGKWFVPYVIEPSAGVDRGVLALLAEAFTREELPNGEERIVLKLKPQLAPIKVAVIPLVKNRPEITEYAKRLKARLLALGLGRVLYEDTGNIGKAYRRHDEVGTPFAVTVDYDTIGQSKDGTTRLKDTVTVRDRDTMEQIRLHVDELEGFLRERLRW 506
               SCOP domains d1b76b2 B:1-394 Glycyl-tRNA synthetase (GlyRS)                                                                                                                                                                                                                                                                                                                                                            d1b76b1 B:395-505 Glycyl-tRNA synthetase (GlyRS), C-terminal domain                                             SCOP domains
               CATH domains 1b76B01 B:1-374 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                                                   ------------------1b76B02 B:393-505  [code=3.40.50.800, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh...eee..hhh......eee.hhhhhhhhhhhhhhhhhhh.............eeehhhhhh...hhhh.......--.....-------------------------------------------------------------...........eee......hhheeee....hhhhhhhhhhhhhhh.........eeeeee..............eeeeee..eee.hhhhhhhhhhhhhhhhhhhhhh...hhheeeee.........eeeeeeeeeee..eeee.eeeeee..hhhhhh....................................eeeeeeeehhhhhhhhhhhheeeee.....eeeee...hhh....eeeee.....hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhh....eeeee.hhhh............eeeeee.....eeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b76 B   1 AASSLDELVALCKRRGFIFQSSEIYGGLQGVYDYGPLGVELKNNLKQAWWRRNVYERDDMEGLDASVLTHRLVLHYSGHEATFADPMVDN--AKARY-------------------------------------------------------------WTPPRYFNMMFQDLRGPRGGRGLLAYLRPETAQGIFVNFKNVLDATSRKLGFGIAQIGKAFRNEITPRNFIFRVREFEQMEIEYFVRPGEDEYWHRYWVEERLKWWQEMGLSRENLVPYQQPPESSAHYAKATVDILYRFPHGSLELEGIAQRTDFDLGSHTKDQEALGITARVLRNEHSTQRLAYRDPETGKWFVPYVIEPSAGVDRGVLALLAEAFTREELPNGEERIVLKLKPQLAPIKVAVIPLVKNRPEITEYAKRLKARLLALGLGRVLYEDTGNIGKAYRRHDEVGTPFAVTVDYDTIGQSKDGTTRLKDTVTVRDRDTMEQIRLHVDELEGFLRERLRW 505
                                    10        20        30        40        50        60        70        80        90  |   |  -         -         -         -         -         -       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     
                                                                                                                    90 91  95                                                           159
   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, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B76)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYG_THET8 | P56206)
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:0004820    glycine-tRNA ligase activity    Catalysis of the reaction: ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).
    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.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0006426    glycyl-tRNA aminoacylation    The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-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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  1b76
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYG_THET8 | P56206: 1ati 1ggm

(-) Related Entries Specified in the PDB File

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