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 :  ASPARTYL-TRNA SYNTHETASE
 
Authors :  E. Schmitt, L. Moulinier, J. -C. Thierry, D. Moras
Date :  27 Jan 99  (Deposition) - 02 Feb 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Synthetase, Trna Ligase, , Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Schmitt, L. Moulinier, S. Fujiwara, T. Imanaka, J. C. Thierry, D. Moras
Crystal Structure Of Aspartyl-Trna Synthetase From Pyrococcus Kodakaraensis Kod: Archaeon Specificity And Catalytic Mechanism Of Adenylate Formation.
Embo J. V. 17 5227 1998
PubMed-ID: 9724658  |  Reference-DOI: 10.1093/EMBOJ/17.17.5227

(-) Compounds

Molecule 1 - PROTEIN (ASPARTYL-TRNA SYNTHETASE)
    Cellular Location: CYTOPLASM
    Chains: A, B
    EC Number: 6.1.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC18F
    Expression System Taxid: 562
    Gene: ASPS
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: KOD1
    Synonym: ASPARTYL TRNA LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MN6Ligand/IonMANGANESE (II) ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREATP A:500 , HOH A:2198 , HOH A:2199 , HOH A:2200 , HOH A:2201BINDING SITE FOR RESIDUE MN A 600
2AC2SOFTWAREGLU A:361 , SER A:364 , ATP A:500 , MN A:602 , HOH A:2250 , HOH A:2251BINDING SITE FOR RESIDUE MN A 601
3AC3SOFTWAREGLU A:361 , ATP A:500 , MN A:601 , HOH A:2248 , HOH A:2249 , HOH A:2250BINDING SITE FOR RESIDUE MN A 602
4AC4SOFTWAREATP B:1500 , HOH B:2194 , HOH B:2195 , HOH B:2196 , HOH B:2197BINDING SITE FOR RESIDUE MN B 1600
5AC5SOFTWAREGLU B:1361 , ATP B:1500 , MN B:1602 , HOH B:2252 , HOH B:2254 , HOH B:2293BINDING SITE FOR RESIDUE MN B 1601
6AC6SOFTWAREGLU B:1361 , SER B:1364 , ATP B:1500 , MN B:1601 , HOH B:2253 , HOH B:2254BINDING SITE FOR RESIDUE MN B 1602
7AC7SOFTWAREARG A:214 , GLU A:216 , ARG A:222 , HIS A:223 , LEU A:224 , GLU A:361 , ILE A:362 , SER A:363 , SER A:364 , GLY A:407 , GLY A:409 , ARG A:412 , MN A:600 , MN A:601 , MN A:602 , HOH A:2148 , HOH A:2191 , HOH A:2199 , HOH A:2200 , HOH A:3114BINDING SITE FOR RESIDUE ATP A 500
8AC8SOFTWAREARG B:1214 , GLU B:1216 , HIS B:1223 , LEU B:1224 , ALA B:1227 , GLU B:1361 , ILE B:1362 , SER B:1363 , SER B:1364 , GLY B:1407 , GLY B:1409 , ARG B:1412 , MN B:1600 , MN B:1601 , MN B:1602 , HOH B:2123 , HOH B:2196 , HOH B:2197 , HOH B:2987BINDING SITE FOR RESIDUE ATP B 1500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B8A)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Thr A:103 -Pro A:104
2Leu A:278 -Pro A:279
3Thr A:437 -Pro A:438
4Thr B:1103 -Pro B:1104
5Leu B:1278 -Pro B:1279
6Thr B:1437 -Pro B:1438

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B8A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B8A)

(-) Exons   (0, 0)

(no "Exon" information available for 1B8A)

(-) 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:438
 aligned with SYD_THEKO | Q52428 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:438
                                    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        
           SYD_THEKO      1 MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIVVLNRAETPLPLDPTGKVKAELDTRLDNRFMDLRRPEVMAIFKIRSSVFKAVRDFFHENGFIEIHTPKIIATATEGGTELFPMKYFEEDAFLAQSPQLYKQIMMASGLDRVYEIAPIFRAEEHNTTRHLNEAWSIDSEMAFIEDEEEVMSFLERLVAHAINYVREHNAKELDILNFELEEPKLPFPRVSYDKALEILGDLGKEIPWGEDIDTEGERLLGKYMMENENAPLYFLYQYPSEAKPFYIMKYDNKPEICRAFDLEYRGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGMPPHGGFGLGAERLIKQMLDLPNIREVILFPRDRRRLTP  438
               SCOP domains d1b8aa1 A:1-103 Aspartyl-tRNA synthetase (AspRS)                                                       d1b8aa2 A:104-438 Aspartyl-tRNA synthetase (AspRS)                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1b8aA01 A:1-105 Nucleic acid-binding proteins                                                            1b8aA02 A:106-438 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhh..hhh...eeeeeeeeeeeeee..eeeeeeee..eeeeeeee.....hhhhhhhhh.....eeeeeeeeee.......eeeee.eeeeee.................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................eeee..eeee.....hhhhhhhhh....eeeeeeeee............eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.hhhhhh............eeeehhhhhhhhhh............hhhhhhhhhhhhhhh...eeeee...hhh................eeeeee..eeeeeeee....hhhhhhhhhh....hhhhhhhhhhh......eeeeeeehhhhhhhh.....hhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1b8a A    1 MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIVVLNRAETPLPLDPTGKVKAELDTRLNNRFMDLRRPEVMAIFKIRSSVFKAVRDFFHENGFIEIHTPKIIATATEGGTELFPMKYFEEDAFLAESPQLYKEIMMASGLDRVYEIAPIFRAEEHNTTRHLNEAWSIDSEMAFIEDEEEVMSFLERLVAHAINYVREHNAKELDILNFELEEPKLPFPRVSYDKALEILGDLGKEIPWGEDIDTEGERLLGKYMMENENAPLYFLYQYPSEAKPFYIMKYDNKPEICRAFDLEYRGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGMPPHGGFGLGAERLIKQMLDLPNIREVILFPRDRRRLTP  438
                                    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        


Chain B from PDB  Type:PROTEIN  Length:438
 aligned with SYD_THEKO | Q52428 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:438
                                    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        
           SYD_THEKO      1 MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIVVLNRAETPLPLDPTGKVKAELDTRLDNRFMDLRRPEVMAIFKIRSSVFKAVRDFFHENGFIEIHTPKIIATATEGGTELFPMKYFEEDAFLAQSPQLYKQIMMASGLDRVYEIAPIFRAEEHNTTRHLNEAWSIDSEMAFIEDEEEVMSFLERLVAHAINYVREHNAKELDILNFELEEPKLPFPRVSYDKALEILGDLGKEIPWGEDIDTEGERLLGKYMMENENAPLYFLYQYPSEAKPFYIMKYDNKPEICRAFDLEYRGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGMPPHGGFGLGAERLIKQMLDLPNIREVILFPRDRRRLTP  438
               SCOP domains d1b8ab1 B:1001-1103 Aspartyl-tRNA synthetase (AspRS)                                                   d1b8ab2 B:1104-1438 Aspartyl-tRNA synthetase (AspRS)                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1b8aB01 B:1001-1105 Nucleic acid-binding proteins                                                        1b8aB02 B:1106-1438 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhh..hhh...eeeeeeeeeeeee...eeeeeeee..eeeeeeeehhh..hhhhhhhhh.....eeeeeeeeee.......eeeee.eeeeee.................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......................eeee..eeee.....hhhhhhhhh....eeeeeeeee............eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh.hhhhhh............eeeehhhhhhhhhhh...........hhhhhhhhhhhhhhh...eeeee...hhh................eeeeee..eeeeeeee....hhhhhhhhhh....hhhhhhhhhhh......eeeeeeehhhhhhhh.....hhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1b8a B 1001 MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIVVLNRAETPLPLDPTGKVKAELDTRLNNRFMDLRRPEVMAIFKIRSSVFKAVRDFFHENGFIEIHTPKIIATATEGGTELFPMKYFEEDAFLAESPQLYKEIMMASGLDRVYEIAPIFRAEEHNTTRHLNEAWSIDSEMAFIEDEEEVMSFLERLVAHAINYVREHNAKELDILNFELEEPKLPFPRVSYDKALEILGDLGKEIPWGEDIDTEGERLLGKYMMENENAPLYFLYQYPSEAKPFYIMKYDNKPEICRAFDLEYRGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGMPPHGGFGLGAERLIKQMLDLPNIREVILFPRDRRRLTP 1438
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390      1400      1410      1420      1430
   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: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) 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 1B8A)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYD_THEKO | Q52428)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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. 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/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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:278 - Pro A:279   [ RasMol ]  
    Leu B:1278 - Pro B:1279   [ RasMol ]  
    Thr A:103 - Pro A:104   [ RasMol ]  
    Thr A:437 - Pro A:438   [ RasMol ]  
    Thr B:1103 - Pro B:1104   [ RasMol ]  
    Thr B:1437 - Pro B:1438   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1b8a
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SYD_THEKO | Q52428
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.1.1.12
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SYD_THEKO | Q52428
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SYD_THEKO | Q52428: 3nel 3nem 3nen

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1B8A)