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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPTOPHANYL TRRNA SYNTHETASE II FROM DEINOCOCCUS RADIODURANS IN COMPLEX WITH L-TRP
 
Authors :  M. R. Buddha, B. R. Crane
Date :  11 Jan 05  (Deposition) - 22 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  B,C  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Auxiliary Tryptophanyl Trna Synthetase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Buddha, B. R. Crane
Structure And Activity Of An Aminoacyl-Trna Synthetase That Charges Trna With Nitro-Tryptophan.
Nat. Struct. Mol. Biol. V. 12 274 2005
PubMed-ID: 15723076  |  Reference-DOI: 10.1038/NSMB907

(-) Compounds

Molecule 1 - TRYPTOPHANYL-TRNA SYNTHETASE
    Chains: B, A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ENZYME
    Gene: DR1093
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: R1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x):  BC
Biological Unit 2 (2x): A  

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1TRP1Ligand/IonTRYPTOPHAN
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1TRP1Ligand/IonTRYPTOPHAN
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1TRP-1Ligand/IonTRYPTOPHAN

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY C:28 , ALA C:61 , GLN C:64 , GLN C:154 , ASP C:157 , ILE C:158BINDING SITE FOR RESIDUE TRP C 3000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YI8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YI8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YI8)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYW2_DEIRA31-40
 
 		  3A:31-40
B:31-40
C:31-40
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYW2_DEIRA31-40
 
 		  2-
B:31-40
C:31-40
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRNA_LIGASE_IPS00178 Aminoacyl-transfer RNA synthetases class-I signature.SYW2_DEIRA31-40
 
 		  2A:31-40
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1YI8)

(-) 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:331
 aligned with SYW2_DEIRA | Q9RVD6 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:331
                                    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 
           SYW2_DEIRA    21 ARPRVLTGDRPTGALHLGHLAGSLQNRVRLQDEAELFVLLADVQALTDHFDRPEQVRENVLAVALDYLAAGLDPQKTTCVVQSAVPELAELTVYFLNLVTVSHLRQNPTVKAEIAQKGYGERVPAGFFVYPVSQAADIAAFGATLVPVGDDQLPMLEQTREIVRRFNALYAPVLAEPQAQLSRVPRLPGLDGQAKMSKSLGNAIALGDSADEVARKVMGMYTDPGHLRASDPGRVEGNPVFTFLDAFDPDPARVQALKDQYRAGGLGDVKVKKHLIDVLNGVLAPIRTRRAEYERDPDAVLRFVTEGTARGREVAAQTLGQVRRAMRLFGH 351
               SCOP domains d1yi8a_ A: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1yi8A02 A:209-316 Tyrosyl-Transfer RNA Synthetase                                                           ----------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.......hhhhhhhhhhhhhhhhhhh.eeeee....hhhhhh.hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhh.........ee...............hhhhh.......hhhhhhhhhh...................hhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------AA_TRNA_LI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yi8 A  21 ARPRVLTGDRPTGALHLGHLAGSLQNRVRLQDEAELFVLLADVQALTDHFDRPEQVRENVLAVALDYLAAGLDPQKTTCVVQSAVPELAELTVYFLNLVTVSHLRQNPTVKAEIAQKGYGERVPAGFFVYPVSQAADIAAFGATLVPVGDDQLPMLEQTREIVRRFNALYAPVLAEPQAQLSRVPRLPGLDGQAKMSKSLGNAIALGDSADEVARKVMGMYTDPGHLRASDPGRVEGNPVFTFLDAFDPDPARVQALKDQYRAGGLGDVKVKKHLIDVLNGVLAPIRTRRAEYERDPDAVLRFVTEGTARGREVAAQTLGQVRRAMRLFGH 351
                                    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 


Chain B from PDB  Type:PROTEIN  Length:331
 aligned with SYW2_DEIRA | Q9RVD6 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:331
                                    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 
           SYW2_DEIRA    21 ARPRVLTGDRPTGALHLGHLAGSLQNRVRLQDEAELFVLLADVQALTDHFDRPEQVRENVLAVALDYLAAGLDPQKTTCVVQSAVPELAELTVYFLNLVTVSHLRQNPTVKAEIAQKGYGERVPAGFFVYPVSQAADIAAFGATLVPVGDDQLPMLEQTREIVRRFNALYAPVLAEPQAQLSRVPRLPGLDGQAKMSKSLGNAIALGDSADEVARKVMGMYTDPGHLRASDPGRVEGNPVFTFLDAFDPDPARVQALKDQYRAGGLGDVKVKKHLIDVLNGVLAPIRTRRAEYERDPDAVLRFVTEGTARGREVAAQTLGQVRRAMRLFGH 351
               SCOP domains d1yi8b_ B: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1yi8B02 B:202-316 Tyrosyl-Transfer RNA Synthetase                                                                  ----------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhh.......eeee...........................hhhhhhhhhhh....................hhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------AA_TRNA_LI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yi8 B  21 ARPRVLTGDRPTGALHLGHLAGSLQNRVRLQDEAELFVLLADVQALTDHFDRPEQVRENVLAVALDYLAAGLDPQKTTCVVQSAVPELAELTVYFLNLVTVSHLRQNPTVKAEIAQKGYGERVPAGFFVYPVSQAADIAAFGATLVPVGDDQLPMLEQTREIVRRFNALYAPVLAEPQAQLSRVPRLPGLDGQAKMSKSLGNAIALGDSADEVARKVMGMYTDPGHLRASDPGRVEGNPVFTFLDAFDPDPARVQALKDQYRAGGLGDVKVKKHLIDVLNGVLAPIRTRRAEYERDPDAVLRFVTEGTARGREVAAQTLGQVRRAMRLFGH 351
                                    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 


Chain C from PDB  Type:PROTEIN  Length:331
 aligned with SYW2_DEIRA | Q9RVD6 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:331
                                    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 
           SYW2_DEIRA    21 ARPRVLTGDRPTGALHLGHLAGSLQNRVRLQDEAELFVLLADVQALTDHFDRPEQVRENVLAVALDYLAAGLDPQKTTCVVQSAVPELAELTVYFLNLVTVSHLRQNPTVKAEIAQKGYGERVPAGFFVYPVSQAADIAAFGATLVPVGDDQLPMLEQTREIVRRFNALYAPVLAEPQAQLSRVPRLPGLDGQAKMSKSLGNAIALGDSADEVARKVMGMYTDPGHLRASDPGRVEGNPVFTFLDAFDPDPARVQALKDQYRAGGLGDVKVKKHLIDVLNGVLAPIRTRRAEYERDPDAVLRFVTEGTARGREVAAQTLGQVRRAMRLFGH 351
               SCOP domains d1yi8c_ C: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1yi8C02 C:220-316 Tyrosyl-Transfer RNA Synthetase                                                ----------------------------------- CATH domains
           Pfam domains (1) tRNA-synt_1b-1yi8C01 C:21-304                                                                                                                                                                                                                                                               ----------------------------------------------- Pfam domains (1)
           Pfam domains (2) tRNA-synt_1b-1yi8C02 C:21-304                                                                                                                                                                                                                                                               ----------------------------------------------- Pfam domains (2)
           Pfam domains (3) tRNA-synt_1b-1yi8C03 C:21-304                                                                                                                                                                                                                                                               ----------------------------------------------- Pfam domains (3)
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhh......eeeeeehhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhh.......eeee...........................hhhhhhhhhhh..................hhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------AA_TRNA_LI----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yi8 C  21 ARPRVLTGDRPTGALHLGHLAGSLQNRVRLQDEAELFVLLADVQALTDHFDRPEQVRENVLAVALDYLAAGLDPQKTTCVVQSAVPELAELTVYFLNLVTVSHLRQNPTVKAEIAQKGYGERVPAGFFVYPVSQAADIAAFGATLVPVGDDQLPMLEQTREIVRRFNALYAPVLAEPQAQLSRVPRLPGLDGQAKMSKSLGNAIALGDSADEVARKVMGMYTDPGHLRASDPGRVEGNPVFTFLDAFDPDPARVQALKDQYRAGGLGDVKVKKHLIDVLNGVLAPIRTRRAEYERDPDAVLRFVTEGTARGREVAAQTLGQVRRAMRLFGH 351
                                    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
   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  (1, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SYW2_DEIRA | Q9RVD6)
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: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: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.
    GO:0004830    tryptophan-tRNA ligase activity    Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
biological process
    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.
    GO:0006436    tryptophanyl-tRNA aminoacylation    The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-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.
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

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

UniProtKB/Swiss-Prot
        SYW2_DEIRA | Q9RVD6: 1yia 1yid 2a4m

(-) Related Entries Specified in the PDB File

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