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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NON-DISCRIMINATING AND ARCHAEAL-TYPE ASPARTYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS
 
Authors :  C. Charron, H. Roy, M. Blaise, R. Giege, D. Kern
Date :  26 Nov 02  (Deposition) - 08 Apr 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Charron, H. Roy, M. Blaise, R. Giege, D. Kern
Non-Discriminating And Discriminating Aspartyl-Trna Synthetases Differ In The Anticodon-Binding Domain
Embo J. V. 22 1632 2003
PubMed-ID: 12660169  |  Reference-DOI: 10.1093/EMBOJ/CDG148
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ASPARTYL-TRNA SYNTHETASE 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1N9W)

(-) Sites  (0, 0)

(no "Site" information available for 1N9W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N9W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N9W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N9W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N9W)

(-) Exons   (0, 0)

(no "Exon" information available for 1N9W)

(-) 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:356
 aligned with SYDND_THET8 | Q5SIC2 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:414
                                    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    
          SYDND_THET8     1 MRVLVRDLKAHVGQEVELLGFLHWRRDLGRIQFLLLRDRSGVVQVVTGGLKLPLPESALRVRGLVVENAKAPGGLEVQAKEVEVLSPALEPTPVEIPKEEWRANPDTLLEYRYVTLRGEKARAPLKVQAALVRGFRRYLDRQDFTEIFTPKVVRAGAEGGSGLFGVDYFEKRAYLAQSPQLYKQIMVGVFERVYEVAPVWRMEEHHTSRHLNEYLSLDVEMGFIADEEDLMRLEEALLAEMLEEALNTAGDEIRLLGATWPSFPQDIPRLTHAEAKRILKEELGYPVGQDLSEEAERLLGEYAKERWGSDWLFVTRYPRSVRPFYTYPEEDGTTRSFDLLFRGLEITSGGQRIHRYEELLESLKAKGMDPEAFHGYLEVFKYGMPPHGGFAIGAERLTQKLLGLPNVRYARAFP 414
               SCOP domains d1n9wa1 A:1-93 Aspartyl-tRNA synthetase (AspRS)                                                               d1n9wa2 A:111-414 Aspartyl-tRNA syntheta                            se (AspRS)                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1n9wA01 A:1-92 Nucleic acid-binding proteins                                                1                 n9wA02 A:93-411 Bira Bifunctional Protei                            n; Domain 2                                                                                                                                                                                                                              --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeeeeeeeee...eeeeeeee..eeeeeeee.........eeeeeeeeee.......eeeeeeeeeeee.......-----------------hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee....----------------------------hhhhhhhhhhhhheeeeeee.-------------..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeehhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeee..hhhhh.............eeeeee..eeeeeeee...hhhhhhhhhhhh..hhhhhhhhhhhhhh....eeeeeeehhhhhhhhh...hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n9w A   1 MRVLVRDLKAHVGQEVELLGFLHWRRDLGRIQFLLLRDRSGVVQVVTGGLKLPLPESALRVRGLVVENAKAPGGLEVQAKEVEVLSPALEPTP-----------------YRYVTLRGEKARAPLKVQAALVRGFRRYLDRQDFTEIFTP----------------------------PQLYKQIMVGVFERVYEVAPV-------------EYLSLDVEMGFIADEEDLMRLEEALLAEMLEEALNTAGDEIRLLGATWPSFPQDIPRLTHAEAKRILKEELGYPVGQDLSEEAERLLGEYAKERWGSDWLFVTRYPRSVRPFYTYPEEDGTTRSFDLLFRGLEITSGGQRIHRYEELLESLKAKGMDPEAFHGYLEVFKYGMPPHGGFAIGAERLTQKLLGLPNVRYARAFP 414
                                    10        20        30        40        50        60        70        80        90  |      -         -|      120       130       140       150         -         -       180       190        |-         -  |    220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410    
                                                                                                                       93               111                                    150                          179                 199           213                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with SYDND_THET8 | Q5SIC2 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:414
                                    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    
          SYDND_THET8     1 MRVLVRDLKAHVGQEVELLGFLHWRRDLGRIQFLLLRDRSGVVQVVTGGLKLPLPESALRVRGLVVENAKAPGGLEVQAKEVEVLSPALEPTPVEIPKEEWRANPDTLLEYRYVTLRGEKARAPLKVQAALVRGFRRYLDRQDFTEIFTPKVVRAGAEGGSGLFGVDYFEKRAYLAQSPQLYKQIMVGVFERVYEVAPVWRMEEHHTSRHLNEYLSLDVEMGFIADEEDLMRLEEALLAEMLEEALNTAGDEIRLLGATWPSFPQDIPRLTHAEAKRILKEELGYPVGQDLSEEAERLLGEYAKERWGSDWLFVTRYPRSVRPFYTYPEEDGTTRSFDLLFRGLEITSGGQRIHRYEELLESLKAKGMDPEAFHGYLEVFKYGMPPHGGFAIGAERLTQKLLGLPNVRYARAFP 414
               SCOP domains d1n9wb1 B:1-97 Aspartyl-tRNA synthetase (AspRS)                                                               d1n9wb2 B:111-414 Aspartyl-tRNA syntheta                             se (AspRS)                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1n9wB01 B:1-92 Nucleic acid-binding proteins                                                1n9wB             02 B:93-411 Bira Bifunctional Protein; D                             omain 2                                                                                                                                                                                                                                 --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh..eeeeeeeeeeeeee..eeeeeeee..eeeeeee..........eeeeeeeeee...hhh.eeeeeeeeeeee...........-------------hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..ee....-----------------------------hhhhhhhhhhhheeeeeee.-------------..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeehhhhhhhhhhh.........hhhhhhhhhhhhhhhh...eeeee....................eeeeee..eeeeeeee...hhhhhhhhhhh.......hhhhhhhhhh....eeeeeeehhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n9w B   1 MRVLVRDLKAHVGQEVELLGFLHWRRDLGRIQFLLLRDRSGVVQVVTGGLKLPLPESALRVRGLVVENAKAPGGLEVQAKEVEVLSPALEPTPVEIP-------------YRYVTLRGEKARAPLKVQAALVRGFRRYLDRQDFTEIFTP-----------------------------QLYKQIMVGVFERVYEVAPV-------------EYLSLDVEMGFIADEEDLMRLEEALLAEMLEEALNTAGDEIRLLGATWPSFPQDIPRLTHAEAKRILKEELGYPVGQDLSEEAERLLGEYAKERWGSDWLFVTRYPRSVRPFYTYPEEDGTTRSFDLLFRGLEITSGGQRIHRYEELLESLKAKGMDPEAFHGYLEVFKYGMPPHGGFAIGAERLTQKLLGLPNVRYARAFP 414
                                    10        20        30        40        50        60        70        80        90      |  -         -|      120       130       140       150         -         -       180       190        |-         -  |    220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410    
                                                                                                                           97           111                                    150                           180                199           213
   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 1N9W)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYDND_THET8 | Q5SIC2)
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:0050560    aspartate-tRNA(Asn) ligase activity    Catalysis of the reaction: tRNA(Asx) + L-aspartate + ATP = aspartyl-tRNA(Asx) + diphosphate + 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: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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 Related Entries

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        SYDND_THET8 | Q5SIC2: 3kfu

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