Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ASPARAGINYL-TRNA SYNTHETASE FROM PYROCOCCUS HORIKOSHII
 
Authors :  W. Iwasaki, S. Sekine, S. Yokoyama, Riken Structural Genomics/Prot Initiative (Rsgi)
Date :  15 May 05  (Deposition) - 23 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Aminoacyl-Trna Synthetase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Iwasaki, S. Sekine, C. Kuroishi, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Structural Basis Of The Water-Assisted Asparagine Recognition By Asparaginyl-Trna Synthetase.
J. Mol. Biol. V. 360 329 2006
PubMed-ID: 16753178  |  Reference-DOI: 10.1016/J.JMB.2006.04.068

(-) Compounds

Molecule 1 - ASPARAGINYL-TRNA SYNTHETASE
    ChainsA
    EC Number6.1.1.22
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11A
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificPYROCOCCUS HORIKOSHII
    Organism Taxid53953
    SynonymASPARAGINE-TRNA LIGASE, ASNRS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1X56)

(-) Sites  (0, 0)

(no "Site" information available for 1X56)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X56)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:277 -Pro A:278
2Tyr A:433 -Pro A:434

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X56)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1X56)

(-) Exons   (0, 0)

(no "Exon" information available for 1X56)

(-) Sequences/Alignments

Asymmetric 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:420
 aligned with SYN_PYRHO | O57980 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:434
                                    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    
            SYN_PYRHO     1 MIEKVYCQEVKPELDGKKVRLAGWVYTNMRVGKKIFLWIRDSTGIVQAVVAKNVVGEETFEKAKKLGRESSVIVEGIVKADERAPGGAEVHVEKLEVIQAVSEFPIPENPEQASPELLLDYRHLHIRTPKASAIMKVKETLIMAAREWLLKDGWHEVFPPILVTGAVEGGATLFKLKYFDKYAYLSQSAQLYLEAAIFGLEKVWSLTPSFRAEKSRTRRHLTEFWHLELEAAWMDLWDIMKVEEELVSYMVQRTLELRKKEIEMFRDDLTTLKNTEPPFPRISYDEAIDILQSKGVNVEWGDDLGADEERVLTEEFDRPFFVYGYPKHIKAFYMKEDPNDPRKVLASDMLAPEGYGEIIGGSQREDDYDKLLNRILEEGMDPKDYEWYLDLRRYGSVPHSGFGLGVERLVAWVLKLDHIRWAALFPRTPARLYP 434
               SCOP domains d1x56a1 A:1-104 automated matches                                                                       d1x56a2 A:105-434 automated matches                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1x56A01 A:1-104 Nucleic acid-binding proteins                                                           1x56A02 A:105-434 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------tRNA_anti-1x56A01 A:19-98                                                       ---------------tRNA-synt_2-1x56A02 A:114-430                                                                                                                                                                                                                                                                                                ---- Pfam domains
         Sec.struct. author .....hhhhhhhhhh..eeeeeeeeeeeeee..eeeeeeee..eeeeeeehhhhhhhhhhhhhhh.....eeeeeeeeee...hhh.eeeeeeeeeeee.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.....eee--------eeeeee..eeeee...hhhhhhhhhhhhheeeeeeeee...------...eeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh......eeehhhhhhhhhhh..........hhhhhhhhhh.....eeeeeee.hhh.....ee..eeeeeeeeeeee....eeeeeeee...hhhhhhhhhhhh......hhhhhhh.......eeeeeeehhhhhhhhh...hhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x56 A   1 MIEKVYCQEVKPELDGKKVRLAGWVYTNMRVGKKIFLWIRDSTGIVQAVVAKNVVGEETFEKAKKLGRESSVIVEGIVKADERAPGGAEVHVEKLEVIQAVSEFPIPENPEQASPELLLDYRHLHIRTPKASAIMKVKETLIMAAREWLLKDGWHEVFPPILVT--------LFKLKYFDKYAYLSQSAQLYLEAAIFGLEKVWSLTPSFRAE------HLTEFWHLELEAAWMDLWDIMKVEEELVSYMVQRTLELRKKEIEMFRDDLTTLKNTEPPFPRISYDEAIDILQSKGVNVEWGDDLGADEERVLTEEFDRPFFVYGYPKHIKAFYMKEDPNDPRKVLASDMLAPEGYGEIIGGSQREDDYDKLLNRILEEGMDPKDYEWYLDLRRYGSVPHSGFGLGVERLVAWVLKLDHIRWAALFPRTPARLYP 434
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   |     -  |    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    
                                                                                                                                                                                             164      173                                     213    220                                                                                                                                                                                                                      

   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 Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: OB (224)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYN_PYRHO | O57980)
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:0004816    asparagine-tRNA ligase activity    Catalysis of the reaction: L-asparagine + ATP + tRNA(Asn) = AMP + Asn-tRNA(Asn) + diphosphate + 2 H(+).
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0006421    asparaginyl-tRNA aminoacylation    The process of coupling asparagine to asparaginyl-tRNA, catalyzed by asparaginyl-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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1x56)
 
  Sites
(no "Sites" information available for 1x56)
 
  Cis Peptide Bonds
    Pro A:277 - Pro A:278   [ RasMol ]  
    Tyr A:433 - Pro A:434   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1x56
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SYN_PYRHO | O57980
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.1.1.22
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SYN_PYRHO | O57980
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SYN_PYRHO | O579801x54 1x55

(-) Related Entries Specified in the PDB File

1x54
1x56 RELATED ID: PHO001000241.1 RELATED DB: TARGETDB