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(-) Description

Title :  ASPARTYL-TRNA SYNTHETASE COMPLEXED WITH ASPARTIC ACID
 
Authors :  E. Schmitt, D. Moras, L. Moulinier
Date :  09 Jun 10  (Deposition) - 04 Aug 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminoacyl-Trna Synthetase, Rossmann Fold Ob Fold, Amino Acid, Mg, Trna, 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 - ASPARTYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: JM101TR
    Expression System Taxid: 562
    Expression System Vector Type: PUC18
    Gene: ASPS, TK0492
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 311400
    Synonym: ASPARTATE--TRNA LIGASE, ASPRS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ASP1Mod. Amino AcidASPARTIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:170 , SER A:190 , GLN A:192 , LYS A:195 , ARG A:214 , TYR A:339 , SER A:364 , GLY A:365 , ARG A:368 , PHE A:406 , GLY A:407 , HOH A:5074 , HOH A:5075BINDING SITE FOR RESIDUE ASP A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NEL)

(-) 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:103 -Pro B:104
5Leu B:278 -Pro B:279
6Thr B:437 -Pro B:438

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NEL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NEL)

(-) Exons   (0, 0)

(no "Exon" information available for 3NEL)

(-) 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:439
 aligned with SYD_THEKO | Q52428 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               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-   -
               SCOP domains d3nela1 A:1-102 automated matches                                                                     d3nela2 A:103-316,A:317-438 automated matches                                                                                                                                                                         d3nela2 A:103-316,A:317-438 automated matches                                                                             - SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh..eeeeeeeeeeeee...eeeeeeee..eeeeeeee....hhhhhhhhhhh....eeeeeeeeee.......eeeeeeeeeeee................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee...........eeee..eeeee...hhhhhhhhhhh...eeeeeeeee............eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee..hhhhh.....ee..eeeee.eeeeee..eeeeeeee...hhhhhhhhhhhh..hhhhhhhhhhh.......eeeeeeehhhhhhhhh...hhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nel A   1 MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIVVLNRAETPLPLDPTGKVKAELDTRLDNRFMDLRRPEVMAIFKIRSSVFKAVRDFFHENGFIEIHTPKIIATATEGGTELFPMKYFEEDAFLAQSPQLYKQIMMASGLDRVYEIAPIFRAEEHNTTRHLNEAWSIDSEMAFIEDEEEVMSFLERLVAHAINYVREHNAKELDILNFELEEPKLPFPRVSYDKALEILGDLGKEIPWGEDIDTEGERLLGKYMMENENAPLYFLYQYPSEAKPFYIMKYDNKPEICRAFDLEYRGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGMPPHGGFGLGAERLIKQMLDLPNIREVILFPRDRRRLTPD 500
                                    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       ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               438|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                500


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 d3nelb1 B:1-102 automated matches                                                                     d3nelb2 B:103-316,B:317-438 automated matches                                                                                                                                                                         d3nelb2 B:103-316,B:317-438 automated matches                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhh..eeeeeeeeeeeee...eeeeeeee..eeeeeeee.hhhhhhhhhhhhhh....eeeeeeeeee.......eeeeeeeeeeee................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee.....ee...........eeee..eeeee...hhhhhhhhhhh...eeeeeeeee............eeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeehhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee..hhhhh.....ee..eeeee.eeeeee..eeeeeeee...hhhhhhhhhhhh..hhhhhhhhhhhhh.....eeeeeeehhhhhhhhh...hhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nel B   1 MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIVVLNRAETPLPLDPTGKVKAELDTRLDNRFMDLRRPEVMAIFKIRSSVFKAVRDFFHENGFIEIHTPKIIATATEGGTELFPMKYFEEDAFLAQSPQLYKQIMMASGLDRVYEIAPIFRAEEHNTTRHLNEAWSIDSEMAFIEDEEEVMSFLERLVAHAINYVREHNAKELDILNFELEEPKLPFPRVSYDKALEILGDLGKEIPWGEDIDTEGERLLGKYMMENENAPLYFLYQYPSEAKPFYIMKYDNKPEICRAFDLEYRGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGMPPHGGFGLGAERLIKQMLDLPNIREVILFPRDRRRLTP 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
   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  (0, 0)

(no "CATH Domain" information available for 3NEL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3NEL)

(-) 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.

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  3nel
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 Related Entries

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

UniProtKB/Swiss-Prot
        SYD_THEKO | Q52428: 1b8a 3nem 3nen

(-) Related Entries Specified in the PDB File

1b8a SAME PROTEIN COMPLEXED WITH ATP-MN
3nem SAME PROTEIN COMPLEXED WITH ASPARTYL-ADENYLATE
3nen SAME PROTEIN UNLIGANDED