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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE ALPHA CHAIN (TM0216) FROM THERMOTOGA MARITIMA AT 1.95 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  05 Jul 02  (Deposition) - 17 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Tm0216, Jcsg, Glycyl-Trna Synthetase Alpha Chain, Psi, Protein Structure Initiative, Joint Center For Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Glycyl-Trna Synthetase Alpha Chain (Tm0216) From Thermotoga Maritima At 1. 95 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCYL-TRNA SYNTHETASE ALPHA CHAIN
    Chains: A, B
    EC Number: 6.1.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0216
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: GLYCINE--TRNA LIGASE ALPHA CHAIN, GLYRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1J5W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J5W)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:82 -Pro A:83
2Lys B:82 -Pro B:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J5W)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_II_GLYABPS50861 Heterodimeric glycyl-transfer RNA synthetases family profile.SYGA_THEMA2-276
 		  2A:2-276
B:2-276

(-) Exons   (0, 0)

(no "Exon" information available for 1J5W)

(-) 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:276
 aligned with SYGA_THEMA | Q9WY59 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:281
                                    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 
           SYGA_THEMA     1 MYLQDVIMKLNDFWASKGCLLEQPYDMEVGAGTFHPATFFGSLRKGPWKVAYVQPSRRPTDGRYGENPNRLQRYFQYQVIIKPSPENSQELYLESLEYLGINLKEHDIRFVEDNWESPTLGAWGVGWEVWLDGMEITQFTYFQQIGGISLKDIPLEITYGLERIAMYLQGVDNVYEVQWNENVKYGDVFLENEREFSVFNFEEANVGLLFRHFDEYEKEFYRLVEKNLYLPAYDYILKCSHTFNLLDARGAISVSQRQTYVKRIQAMARKAARVFLEVQAN 281
               SCOP domains d1j5wa_ A: Glycyl-tRNA synthetase (GlyRS) alpha chain                                                                                                                                                                                                                                     SCOP domains
               CATH domains -1j5wA01 A:2-204 Bira Bifunctional Protein; Domain 2                                                                                                                                                        1j5wA02 A:205-281 Class II aaRS and biotin synthetases; domain 2              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..ee.........hhhhhhhhhhhhhh...eeeeeeeeee...-----.......eeeeeeeeee....hhhhhhhhhhhhh........eeeeee..eehhhheeeeeeeeee..eeeeeeeeeee..........eeeeeehhhhhhhhhh..hhhh.eee..eehhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -AA_TRNA_LIGASE_II_GLYAB  PDB: A:2-276 UniProt: 2-276                                                                                                                                                                                                                               ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j5w A   1 mYLQDVImKLNDFWASKGCLLEQPYDmEVGAGTFHPATFFGSLRKGPWKVAYVQPSRRPT-----ENPNRLQRYFQYQVIIKPSPENSQELYLESLEYLGINLKEHDIRFVEDNWESPTLGAWGVGWEVWLDGmEITQFTYFQQIGGISLKDIPLEITYGLERIAmYLQGVDNVYEVQWNENVKYGDVFLENEREFSVFNFEEANVGLLFRHFDEYEKEFYRLVEKNLYLPAYDYILKCSHTFNLLDARGAISVSQRQTYVKRIQAmARKAARVFLEVQAN 281
                            |      |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 
                            |      8-MSE             27-MSE                           60    66                                                                 134-MSE                         166-MSE                                                                                              267-MSE          
                            1-MSE                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:278
 aligned with SYGA_THEMA | Q9WY59 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:280
                                    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
           SYGA_THEMA     1 MYLQDVIMKLNDFWASKGCLLEQPYDMEVGAGTFHPATFFGSLRKGPWKVAYVQPSRRPTDGRYGENPNRLQRYFQYQVIIKPSPENSQELYLESLEYLGINLKEHDIRFVEDNWESPTLGAWGVGWEVWLDGMEITQFTYFQQIGGISLKDIPLEITYGLERIAMYLQGVDNVYEVQWNENVKYGDVFLENEREFSVFNFEEANVGLLFRHFDEYEKEFYRLVEKNLYLPAYDYILKCSHTFNLLDARGAISVSQRQTYVKRIQAMARKAARVFLEVQA 280
               SCOP domains d1j5wb_ B: Glycyl-tRNA synthetase (GlyRS) alpha chain                                                                                                                                                                                                                                    SCOP domains
               CATH domains -1j5wB01 B:2-204 Bira Bifunctional Protein; Domain 2                                                                                                                                                        1j5wB02 B:205-280 Class II aaRS and biotin synthetases; domain 2             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...ee.........hhhhhhhhhhhhhh...eeeeeeeeee.hhhh..........eeeeeeeeee....hhhhhhhhhhhhhh.--....eeeee..eeehhhheeeeeeeeee...eeeeeeeeee..........eeeeeehhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -AA_TRNA_LIGASE_II_GLYAB  PDB: B:2-276 UniProt: 2-276                                                                                                                                                                                                                               ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j5w B   1 mYLQDVImKLNDFWASKGCLLEQPYDmEVGAGTFHPATFFGSLRKGPWKVAYVQPSRRPTDGRYGENPNRLQRYFQYQVIIKPSPENSQELYLESLEYLGI--KEHDIRFVEDNWESPTLGAWGVGWEVWLDGmEITQFTYFQQIGGISLKDIPLEITYGLERIAmYLQGVDNVYEVQWNENVKYGDVFLENEREFSVFNFEEANVGLLFRHFDEYEKEFYRLVEKNLYLPAYDYILKCSHTFNLLDARGAISVSQRQTYVKRIQAmARKAARVFLEVQA 280
                            |      |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
                            1-MSE  8-MSE             27-MSE                                                                   101  |                           134-MSE                         166-MSE                                                                                              267-MSE         
                                                                                                                                 104
   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  (1, 2)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J5W)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYGA_THEMA | Q9WY59)
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.
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: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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