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(-) Description

Title :  CRYSTAL STRUCTURE OF DTD FROM PLASMODIUM FALCIPARUM
 
Authors :  Y. Manickam, T. K. Bhatt, A. Sharma
Date :  12 Nov 09  (Deposition) - 08 Dec 09  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Dtd, D-Amino Acid, Deacylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. K. Bhatt, M. Yogavel, S. Wydau, R. Berwal, A. Sharma
Ligand-Bound Structures Provide Atomic Snapshots For The Catalytic Mechanism Of D-Amino Acid Deacylase
J. Biol. Chem. V. 285 5917 2010
PubMed-ID: 20007323  |  Reference-DOI: 10.1074/JBC.M109.038562

(-) Compounds

Molecule 1 - D-TYROSYL-TRNA(TYR) DEACYLASE
    Chains: A, B, C, D, E, F
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DTD
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3KNP)

(-) Sites  (0, 0)

(no "Site" information available for 3KNP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:149 -Pro A:150
2Gly B:149 -Pro B:150
3Gly C:149 -Pro C:150
4Gly D:149 -Pro D:150
5Gly E:149 -Pro E:150
6Gly F:149 -Pro F:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KNP)

(-) 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:159
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3knpA00 A:1-159  [code=3.50.80.10, no name defined]                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee..........eeeeeee..eeeeeee.....hhhhhhhhhhhhhhheee........ee......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.ee.......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knp A   1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3knpB00 B:1-160  [code=3.50.80.10, no name defined]                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee..........eeeeeee..eeeeee......hhhhhhhhhhhhh....eee..eeeee.......eeeeee.hhhhh........hhhhh.hhhhhhhhhhhhhhhhhhh.....eee......eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knp B   1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160


Chain C from PDB  Type:PROTEIN  Length:159
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3knpC00 C:1-159  [code=3.50.80.10, no name defined]                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee..........eeeeeee..eeeeeee.....hhhhhhhhhhhhhhheee........ee.hhhh.eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhh............eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knp C   1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         


Chain D from PDB  Type:PROTEIN  Length:152
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:160
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3knpD00 D:1-160  [        code=3.50.80.10, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee...--------.eeeeee..eeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knp D   1 MRVVIQRVKGAILSVRKE--------LEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10       | -      | 30        40        50        60        70        80        90       100       110       120       130       140       150       160
                                            18       27                                                                                                                                     


Chain E from PDB  Type:PROTEIN  Length:148
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTH 158
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3knpE00 E:1-158            [code=3.50.80.10, no name defined]                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.----------.eeeeee..eeeeee......hhhhhhhhhhhhhhh...................eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knp E   1 MRVVIQRVKGAILSVR----------LEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTH 158
                                    10     |   -      | 30        40        50        60        70        80        90       100       110       120       130       140       150        
                                          16         27                                                                                                                                   


Chain F from PDB  Type:PROTEIN  Length:149
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3knpF00 F:1-159            [code=3.50.80.10, no name defined]                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.----------.eeeeee..eeeeeee.....hhhhhhhhhhhhhhheeeee..eeeeee.hhhh.eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhh.....eee......eeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knp F   1 MRVVIQRVKGAILSVR----------LEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHD 159
                                    10     |   -      | 30        40        50        60        70        80        90       100       110       120       130       140       150         
                                          16         27
   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  (0, 0)

(no "SCOP Domain" information available for 3KNP)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q8IIS0_PLAF7 | Q8IIS0)
molecular function
    GO:0051500    D-tyrosyl-tRNA(Tyr) deacylase activity    Catalysis of the reaction: D-tyrosyl-tRNA(Tyr) = D-tyrosine + tRNA(Tyr). Hydrolysis of the removal of D-tyrosine from tyrosine residues in charged tRNA.
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    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:0019478    D-amino acid catabolic process    The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.
    GO:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.
    GO:0006399    tRNA metabolic process    The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.
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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(no "Sites" information available for 3knp)
 
  Cis Peptide Bonds
    Gly A:149 - Pro A:150   [ RasMol ]  
    Gly B:149 - Pro B:150   [ RasMol ]  
    Gly C:149 - Pro C:150   [ RasMol ]  
    Gly D:149 - Pro D:150   [ RasMol ]  
    Gly E:149 - Pro E:150   [ RasMol ]  
    Gly F:149 - Pro F:150   [ RasMol ]  
 
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  3knp
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  3.1.-.-
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3knf 3knp 3ko4 3ko5 3ko7 3ko9 3kob 3koc 3kod