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(-) Description

Title :  D-AMINOACYL-TRNA DEACYLASE (DTD) FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH D-TYROSYL-3'-AMINOADENOSINE AT 1.86 ANGSTROM RESOLUTION
 
Authors :  S. Ahmad, S. B. Routh, V. Kamarthapu, R. Sankaranarayanan
Date :  23 Oct 13  (Deposition) - 18 Dec 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dtd, Deacylase, Dtd-Like, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ahmad, S. B. Routh, V. Kamarthapu, J. Chalissery, S. Muthukumar, T. Hussain, S. P. Kruparani, M. V. Deshmukh, R. Sankaranarayanan
Mechanism Of Chiral Proofreading During Translation Of The Genetic Code.
Elife V. 2 01519 2013
PubMed-ID: 24302572  |  Reference-DOI: 10.7554/ELIFE.01519

(-) Compounds

Molecule 1 - D-TYROSYL-TRNA(TYR) DEACYLASE
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DTD, PF11_0095
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1D3Y2Ligand/Ion3'-DEOXY-3'-(D-TYROSYLAMINO)ADENOSINE
2PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:41 , ILE A:43 , SER A:87 , GLN A:88 , PHE A:89 , LYS A:107 , ALA A:112 , PHE A:137 , GLY A:138 , ASN A:139 , HOH A:648 , HOH A:705 , GLY B:149 , PRO B:150BINDING SITE FOR RESIDUE D3Y A 201
2AC2SOFTWAREASP A:144 , THR A:146 , GLY B:10 , ILE B:12 , THR B:146BINDING SITE FOR RESIDUE PGE A 502
3AC3SOFTWAREGLY A:149 , PRO A:150 , LEU B:41 , ILE B:43 , SER B:87 , GLN B:88 , PHE B:89 , LYS B:107 , PHE B:137 , GLY B:138 , ASN B:139 , HOH B:343 , HOH B:345 , HOH B:368 , HOH B:393BINDING SITE FOR RESIDUE D3Y B 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NBI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:149 -Pro A:150
2Gly B:149 -Pro B:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NBI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NBI)

(-) Exons   (0, 0)

(no "Exon" information available for 4NBI)

(-) 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:163
                                                                                                                                                                                                   
               SCOP domains d4nbia_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee..........eeeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.hhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbi A   1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDINLN 163
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   


Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains d4nbib_ B: automated matches                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nbi B   1 MRVVIQRVKGAILSVRKLEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10      ||29        39        49        59        69        79        89        99       109       119       129       139       149       159 
                                           17|                                                                                                                                     
                                            27
   Legend:   → Mismatch (orange background)
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  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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NBI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NBI)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:149 - Pro A:150   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q8IIS0_PLAF7 | Q8IIS0: 3knf 3knp 3ko3 3ko4 3ko5 3ko7 3ko9 3kob 3koc 3kod 3lmt 3lmu 3lmv 4nbj 5j61

(-) Related Entries Specified in the PDB File

4nbj