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

(-) Description

Title :  THE ACTIVE SITE OF YEAST ASPARTYL-TRNA SYNTHETASE: STRUCTURAL AND FUNCTIONAL ASPECTS OF THE AMINOACYLATION REACTION
 
Authors :  J. Cavarelli, B. Rees, J. C. Thierry, D. Moras
Date :  19 Jan 95  (Deposition) - 08 May 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,R,S
Keywords :  Complex (Aminoacyl-Trna Synthase/Trna) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Cavarelli, G. Eriani, B. Rees, M. Ruff, M. Boeglin, A. Mitschler, F. Martin, J. Gangloff, J. C. Thierry, D. Moras
The Active Site Of Yeast Aspartyl-Trna Synthetase: Structural And Functional Aspects Of The Aminoacylation Reaction.
Embo J. V. 13 327 1994
PubMed-ID: 8313877
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - T-RNA (75-MER)
    ChainsR, S
    EC Number6.1.1.12
    EngineeredYES
    SyntheticYES
 
Molecule 2 - ASPARTYL-TRNA SYNTHETASE
    ChainsA, B
    EngineeredYES
    Organism ScientificSACCHAROMYCES CEREVISIAE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABRS

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric/Biological Unit (6, 18)
No.NameCountTypeFull Name
11MG2Mod. Nucleotide1N-METHYLGUANOSINE-5'-MONOPHOSPHATE
25MC2Mod. Nucleotide5-METHYLCYTIDINE-5'-MONOPHOSPHATE
35MU2Mod. Nucleotide5-METHYLURIDINE 5'-MONOPHOSPHATE
4ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
5H2U4Mod. Nucleotide5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
6PSU6Mod. NucleotidePSEUDOURIDINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:325 , HIS A:334 , MET A:335 , PHE A:338 , GLU A:478 , ILE A:479 , LEU A:480 , GLY A:526 , ARG A:531 , C R:675 , A R:676BINDING SITE FOR RESIDUE ATP A 701
2AC2SOFTWAREARG B:325 , MET B:335 , PHE B:338 , GLU B:478 , ILE B:479 , LEU B:480 , SER B:481 , ILE B:527 , ARG B:531 , C S:675 , A S:676BINDING SITE FOR RESIDUE ATP B 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:556 -Pro A:557
2Arg B:556 -Pro B:557

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLL018C1YLL018C.1XII:111574-1099011674SYDC_YEAST1-5575572A:68-557
B:68-557
490
490

(-) 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:490
 aligned with SYDC_YEAST | P04802 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:490
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557
           SYDC_YEAST    68 EDTAKDNYGKLPLIQSRDSDRTGQKRVKFVDLDEAKDSDKEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISETPEALPILLEDASRSEAEAEAAGLPVVNLDTRLDYRVIDLRTVTNQAIFRIQAGVCELFREYLATKKFTEVHTPKLLGAPSEGGSSVFEVTYFKGKAYLAQSPQFNKQQLIVADFERVYEIGPVFRAENSNTHRHMTEFTGLDMEMAFEEHYHEVLDTLSELFVFIFSELPKRFAHEIELVRKQYPVEEFKLPKDGKMVRLTYKEGIEMLRAAGKEIGDFEDLSTENEKFLGKLVRDKYDTDFYILDKFPLEIRPFYTMPDPANPKYSNSYDFFMRGEEILSGAQRIHDHALLQERMKAHGLSPEDPGLKDYCDGFSYGCPPHAGGGIGLERVVMFYLDLKNIRRASLFPRDPKRLRP 557
               SCOP domains d1asza1 A:68-204 Aspartyl-tRNA synthetase (AspRS)                                                                                        d1asza2 A:205-557 Aspartyl-tRNA synthetase (AspRS)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1aszA01 A:68-204 Nucleic acid-binding proteins                                                                                           1aszA02 A:205-557 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..................hhh.........eeeeeeeeeeeee....eeeeeeee..eeeeeeee........hhhhhhhhh.....eeeeeeeeee............eeeee.eeeeee.........hhhhh..hhhhh........hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh......................................hhhhhhhhh....eeeeeeeee............eeeeeeeeee....hhhhhhhhhhhhhhhh..hhhh.hhhhhhhh................eeeehhhhhhhhhhh...........hhhhhhhhhhhhhhh...eeeee.......................eeeee..eeeeeeee....hhhhhhhhhh.......hhhhhhhhhh......eeeeeeehhhhhhhhh.....hhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:68-557 UniProt: 1-557 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                        Transcript 1
                 1asz A  68 EDTAKDNYGKLPLIQSRDSDRTGQKRVKFVDLDEAKDSDKEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISETPEALPILLEDASRSEAEAEAAGLPVVNLDTRLDYRVIDLRTVTNQAIFRIQAGVCELFREYLATKKFTEVHTPKLLGAPSEGGSSVFEVTYFKGKAYLAQSPQFNKQQLIVADFERVYEIGPVFRAENSNTHRHMTEFTGLDMEMAFEEHYHEVLDTLSELFVFIFSELPKRFAHEIELVRKQYPVEEFKLPKDGKMVRLTYKEGIEMLRAAGKEIGDFEDLSTENEKFLGKLVRDKYDTDFYILDKFPLEIRPFYTMPDPANPKYSNSYDFFMRGEEILSGAQRIHDHALLQERMKAHGLSPEDPGLKDYCDGFSYGCPPHAGGGIGLERVVMFYLDLKNIRRASLFPRDPKRLRP 557
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557

Chain B from PDB  Type:PROTEIN  Length:490
 aligned with SYDC_YEAST | P04802 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:490
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557
           SYDC_YEAST    68 EDTAKDNYGKLPLIQSRDSDRTGQKRVKFVDLDEAKDSDKEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISETPEALPILLEDASRSEAEAEAAGLPVVNLDTRLDYRVIDLRTVTNQAIFRIQAGVCELFREYLATKKFTEVHTPKLLGAPSEGGSSVFEVTYFKGKAYLAQSPQFNKQQLIVADFERVYEIGPVFRAENSNTHRHMTEFTGLDMEMAFEEHYHEVLDTLSELFVFIFSELPKRFAHEIELVRKQYPVEEFKLPKDGKMVRLTYKEGIEMLRAAGKEIGDFEDLSTENEKFLGKLVRDKYDTDFYILDKFPLEIRPFYTMPDPANPKYSNSYDFFMRGEEILSGAQRIHDHALLQERMKAHGLSPEDPGLKDYCDGFSYGCPPHAGGGIGLERVVMFYLDLKNIRRASLFPRDPKRLRP 557
               SCOP domains d1aszb1 B:68-204 Aspartyl-tRNA synthetase (AspRS)                                                                                        d1aszb2 B:205-557 Aspartyl-tRNA synthetase (AspRS)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1aszB01 B:68-204 Nucleic acid-binding proteins                                                                                           1aszB02 B:205-557 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eee..................hhh..hhhh...eeeeeee............eeeee....eeeee..........hhhhhhhhh.....eeeeeeeeee............eeeee.eeeeee.........hhhhh..hhhhhh.......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................eeee..eeee.....hhhhhhhhh.....eeeeeeee............eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhh................eeeehhhhhhhhhhh...........hhhhhhhhhhhhhh....eeeee......................eeeeee..eeeeeee.....hhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:68-557 UniProt: 1-557 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                                        Transcript 1
                 1asz B  68 EDTAKDNYGKLPLIQSRDSDRTGQKRVKFVDLDEAKDSDKEVLFRARVHNTRQQGATLAFLTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQNLEIHITKIYTISETPEALPILLEDASRSEAEAEAAGLPVVNLDTRLDYRVIDLRTVTNQAIFRIQAGVCELFREYLATKKFTEVHTPKLLGAPSEGGSSVFEVTYFKGKAYLAQSPQFNKQQLIVADFERVYEIGPVFRAENSNTHRHMTEFTGLDMEMAFEEHYHEVLDTLSELFVFIFSELPKRFAHEIELVRKQYPVEEFKLPKDGKMVRLTYKEGIEMLRAAGKEIGDFEDLSTENEKFLGKLVRDKYDTDFYILDKFPLEIRPFYTMPDPANPKYSNSYDFFMRGEEILSGAQRIHDHALLQERMKAHGLSPEDPGLKDYCDGFSYGCPPHAGGGIGLERVVMFYLDLKNIRRASLFPRDPKRLRP 557
                                    77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557

Chain R from PDB  Type:RNA  Length:75
                                                                                                           
                 1asz R 601 UCCGUGAUAGUUuAAuGGuCAGAAUGGGCGCuUGUCgCGUGCCAGAUcGGGGuuCAAUUCCCCGUCGCGGAGCCA 676
                                   610  |  | 620       630 |    |640     ||651  ||   661       671     
                                      613-PSU |          632-PSU|      646||    ||                     
                                         616-H2U              637-1MG   648|    ||                     
                                            619-H2U                      649-5MC||                     
                                                                              654-5MU                  
                                                                               655-PSU                 

Chain S from PDB  Type:RNA  Length:75
                                                                                                           
                 1asz S 601 UCCGUGAUAGUUuAAuGGuCAGAAUGGGCGCuUGUCgCGUGCCAGAUcGGGGuuCAAUUCCCCGUCGCGGAGCCA 676
                                   610  |  | 620       630 |    |640     ||651  ||   661       671     
                                      613-PSU |          632-PSU|      646||    ||                     
                                         616-H2U              637-1MG   648|    ||                     
                                            619-H2U                      649-5MC||                     
                                                                              654-5MU                  
                                                                               655-PSU                 

   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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYDC_YEAST | P04802)
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:0004815    aspartate-tRNA ligase activity    Catalysis of the reaction: ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp).
    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:0006422    aspartyl-tRNA aminoacylation    The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-tRNA synthetase. The aspartyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an aspartic acid accetping 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 and the alpha carboxylic acid group of an amino acid, 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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    1MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    5MC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    5MU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    H2U  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PSU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:556 - Pro A:557   [ RasMol ]  
    Arg B:556 - Pro B:557   [ RasMol ]  
 

(-) 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
  1asz
    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
  SYDC_YEAST | P04802
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.1.1.12
    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
  SYDC_YEAST | P04802
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SYDC_YEAST | P048021asy 1eov

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1ASZ)