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(-) Description

Title :  PRELIMINARY STRUCTURE OF THERMUS THERMOPHILUS LIGAND-FREE VALYL-TRNA SYNTHETASE
 
Authors :  S. Fukai, O. Nureki, S. Sekine, A. Shimada, D. G. Vassylyev, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  10 Sep 02  (Deposition) - 17 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rossmann Fold, Coiled Coil, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Fukai, O. Nureki, S. Sekine, A. Shimada, D. G. Vassylyev, S. Yokoyama
Mechanism Of Molecular Interactions For Trna(Val) Recognition By Valyl-Trna Synthetase
Rna V. 9 100 2003
PubMed-ID: 12554880  |  Reference-DOI: 10.1261/RNA.2760703
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VALYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1IYW)

(-) Sites  (0, 0)

(no "Site" information available for 1IYW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYV_THETH43-54
 		  2A:43-54
B:43-54
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYV_THETH43-54
 		  1A:43-54
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYV_THETH43-54
 		  1-
B:43-54

(-) Exons   (0, 0)

(no "Exon" information available for 1IYW)

(-) Sequences/Alignments

Asymmetric Unit
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  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:862
 aligned with SYV_THETH | P96142 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:862
                                    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       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860  
            SYV_THETH     1 MDLPKAYDPKSVEPKWAEKWAKNPFVANPKSGKPPFVIFMPPPNVTGSLHMGHALDNSLQDALIRYKRMRGFEAVWLPGTDHAGIATQVVVERLLLKEGKTRHDLGREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRYYHEGLAYRAPRLVNWCPRCETTLSDLEVETEPTPGKLYTLRYEVEGGGFIEIATVRPETVFADQAIAVHPEDERYRHLLGKRARIPLTEVWIPILADPAVEKDFGTGALKVTPAHDPLDYEIGERHGLKPVSVINLEGRMEGERVPEALRGLDRFEARRKAVELFREAGHLVKEEDYTIALATCSRCGTPIEYAIFPQWWLRMRPLAEEVLKGLRRGDIAFVPERWKKVNMDWLENVKDWNISRQLWWGHQIPAWYCEDCQAVNVPRPERYLEDPTSCEACGSPRLKRDEDVFDTWFSSALWPLSTLGWPEETEDLKAFYPGDVLVTGYDILFLWVSRMEVSGYHFMGERPFKTVLLHGLVLDEKGQKMSKSKGNVIDPLEMVERYGADALRFALIYLATGGQDIRLDLRWLEMARNFANKLYNAARFVLLSREGFQAKEDTPTLADRFMRSRLSRGVEEITALYEALDLAQAAREVYELVWSEFCDWYLEAAKPALKAGNAHTLRTLEEVLAVLLKLLHPMMPFLTSELYQALTGKEELALEAWPEPGGRDEEAERAFEALKQAVTAVRALKAEAGLPPAQEVRVYLEGETAPVEENLEVFRFLSRADLLPERPAKALVKAMPRVTARMPLEGLLDVEEWRRRQEKRLKELLALAERSQRKLASPGFREKAPKEVVEAEEARLKENLEQAERIREALSQIG 862
               SCOP domains d1iywa4 A:1-189,A:343-578 Valyl-tRNA synthetase (ValRS)                                                                                                                                      d1iywa3 A:190-342 Valyl-tRNA synthetase (ValRS)                                                                                                          d1iywa4 A:1-189,A:343-578 Valyl-tRNA synthetase (ValRS)                                                                                                                                                                                     d1iywa2 A:579-796 Valyl-tRNA synthetase (ValRS)                                                                                                                                                                           d1iywa1 A:797-862 Valyl-tRNA synthetase (ValRS) C-terminal domain  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------AA_TRNA_LIGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iyw A   1 MDLPKAYDPKSVEPKWAEKWAKNPFVANPKSGKPPFVIFMPPPNVTGSLHMGHALDNSLQDALIRYKRMRGFEAVWLPGTDHAGIATQVVVERLLLKEGKTRHDLGREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRYYHEGLAYRAPRLVNWCPRCETTLSDLEVETEPTPGKLYTLRYEVEGGGFIEIATVRPETVFADQAIAVHPEDERYRHLLGKRARIPLTEVWIPILADPAVEKDFGTGALKVTPAHDPLDYEIGERHGLKPVSVINLEGRMEGERVPEALRGLDRFEARRKAVELFREAGHLVKEEDYTIALATCSRCGTPIEYAIFPQWWLRMRPLAEEVLKGLRRGDIAFVPERWKKVNMDWLENVKDWNISRQLWWGHQIPAWYCEDCQAVNVPRPERYLEDPTSCEACGSPRLKRDEDVFDTWFSSALWPLSTLGWPEETEDLKAFYPGDVLVTGYDILFLWVSRMEVSGYHFMGERPFKTVLLHGLVLDEKGQKMSKSKGNVIDPLEMVERYGADALRFALIYLATGGQDIRLDLRWLEMARNFANKLYNAARFVLLSREGFQAKEDTPTLADRFMRSRLSRGVEEITALYEALDLAQAAREVYELVWSEFCDWYLEAAKPALKAGNAHTLRTLEEVLAVLLKLLHPMMPFLTSELYQALTGKEELALEAWPEPGGRDEEAERAFEALKQAVTAVRALKAEAGLPPAQEVRVYLEGETAPVEENLEVFRFLSRADLLPERPAKALVKAMPRVTARMPLEGLLDVEEWRRRQEKRLKELLALAERSQRKLASPGFREKAPKEVVEAEEARLKENLEQAERIREALSQIG 862
                                    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       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860  


Chain B from PDB  Type:PROTEIN  Length:862
 aligned with SYV_THETH | P96142 from UniProtKB/Swiss-Prot  Length:862

    Alignment length:862
                                    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       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860  
            SYV_THETH     1 MDLPKAYDPKSVEPKWAEKWAKNPFVANPKSGKPPFVIFMPPPNVTGSLHMGHALDNSLQDALIRYKRMRGFEAVWLPGTDHAGIATQVVVERLLLKEGKTRHDLGREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRYYHEGLAYRAPRLVNWCPRCETTLSDLEVETEPTPGKLYTLRYEVEGGGFIEIATVRPETVFADQAIAVHPEDERYRHLLGKRARIPLTEVWIPILADPAVEKDFGTGALKVTPAHDPLDYEIGERHGLKPVSVINLEGRMEGERVPEALRGLDRFEARRKAVELFREAGHLVKEEDYTIALATCSRCGTPIEYAIFPQWWLRMRPLAEEVLKGLRRGDIAFVPERWKKVNMDWLENVKDWNISRQLWWGHQIPAWYCEDCQAVNVPRPERYLEDPTSCEACGSPRLKRDEDVFDTWFSSALWPLSTLGWPEETEDLKAFYPGDVLVTGYDILFLWVSRMEVSGYHFMGERPFKTVLLHGLVLDEKGQKMSKSKGNVIDPLEMVERYGADALRFALIYLATGGQDIRLDLRWLEMARNFANKLYNAARFVLLSREGFQAKEDTPTLADRFMRSRLSRGVEEITALYEALDLAQAAREVYELVWSEFCDWYLEAAKPALKAGNAHTLRTLEEVLAVLLKLLHPMMPFLTSELYQALTGKEELALEAWPEPGGRDEEAERAFEALKQAVTAVRALKAEAGLPPAQEVRVYLEGETAPVEENLEVFRFLSRADLLPERPAKALVKAMPRVTARMPLEGLLDVEEWRRRQEKRLKELLALAERSQRKLASPGFREKAPKEVVEAEEARLKENLEQAERIREALSQIG 862
               SCOP domains d1iywb4 B:1-189,B:343-578 Valyl-tRNA synthetase (ValRS)                                                                                                                                      d1iywb3 B:190-342 Valyl-tRNA synthetase (ValRS)                                                                                                          d1iywb4 B:1-189,B:343-578 Valyl-tRNA synthetase (ValRS)                                                                                                                                                                                     d1iywb2 B:579-796 Valyl-tRNA synthetase (ValRS)                                                                                                                                                                           d1iywb1 B:797-862 Valyl-tRNA synthetase (ValRS) C-terminal domain  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------AA_TRNA_LIGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iyw B   1 MDLPKAYDPKSVEPKWAEKWAKNPFVANPKSGKPPFVIFMPPPNVTGSLHMGHALDNSLQDALIRYKRMRGFEAVWLPGTDHAGIATQVVVERLLLKEGKTRHDLGREKFLERVWQWKEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSRYYHEGLAYRAPRLVNWCPRCETTLSDLEVETEPTPGKLYTLRYEVEGGGFIEIATVRPETVFADQAIAVHPEDERYRHLLGKRARIPLTEVWIPILADPAVEKDFGTGALKVTPAHDPLDYEIGERHGLKPVSVINLEGRMEGERVPEALRGLDRFEARRKAVELFREAGHLVKEEDYTIALATCSRCGTPIEYAIFPQWWLRMRPLAEEVLKGLRRGDIAFVPERWKKVNMDWLENVKDWNISRQLWWGHQIPAWYCEDCQAVNVPRPERYLEDPTSCEACGSPRLKRDEDVFDTWFSSALWPLSTLGWPEETEDLKAFYPGDVLVTGYDILFLWVSRMEVSGYHFMGERPFKTVLLHGLVLDEKGQKMSKSKGNVIDPLEMVERYGADALRFALIYLATGGQDIRLDLRWLEMARNFANKLYNAARFVLLSREGFQAKEDTPTLADRFMRSRLSRGVEEITALYEALDLAQAAREVYELVWSEFCDWYLEAAKPALKAGNAHTLRTLEEVLAVLLKLLHPMMPFLTSELYQALTGKEELALEAWPEPGGRDEEAERAFEALKQAVTAVRALKAEAGLPPAQEVRVYLEGETAPVEENLEVFRFLSRADLLPERPAKALVKAMPRVTARMPLEGLLDVEEWRRRQEKRLKELLALAERSQRKLASPGFREKAPKEVVEAEEARLKENLEQAERIREALSQIG 862
                                    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       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860
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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  (4, 8)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SYV_THETH | P96142)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
    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: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:0004832    valine-tRNA ligase activity    Catalysis of the reaction: L-valine + ATP + tRNA(Val) = L-valyl-tRNA(Val) + AMP + diphosphate + 2 H(+).
biological process
    GO:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.
    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.
    GO:0006438    valyl-tRNA aminoacylation    The process of coupling valine to valyl-tRNA, catalyzed by valyl-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.
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
        SYV_THETH | P96142: 1gax 1ivs 1wk9 1wka

(-) Related Entries Specified in the PDB File

1gax 1GAX CONTAINS THE SAME PROTEIN COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE
1ivs 1IVS CONTAINS THE SAME PROTEIN COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE RELATED ID: TRT001000468.1 RELATED DB: TARGETDB