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(-) Description

Title :  CRYSTAL STRUCTURE OF D-TYR-TRNA(TYR) DEACYLASE FROM PLASMODIUM FALCIPARUM
 
Authors :  Y. Manickam, T. K. Bhatt, A. Sharma
Date :  12 Nov 09  (Deposition) - 01 Dec 09  (Release) - 02 Mar 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
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 :  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
    ChainsA, B, C, D, E, F
    EC Number3.1.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDTD
    Organism ScientificPLASMODIUM FALCIPARUM
    Organism Taxid36329
    Strain3D7

 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 3KNF)

(-) Sites  (0, 0)

(no "Site" information available for 3KNF)

(-) SS Bonds  (0, 0)

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

(-) 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 3KNF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KNF)

(-) 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:151
 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 d3knfa_ A: autom         ated matches                                                                                                                            SCOP domains
               CATH domains 3knfA00 A:1-160           [code=3.50.80.10, no name defined]                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.---------..eeeeeeeeeeeeeee.....hhhhhhhhhhhhhhh...................eeeeee.hhhh.................hhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knf A   1 MRVVIQRVKGAILSVR---------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10     |   -     |  30        40        50        60        70        80        90       100       110       120       130       140       150       160
                                          16        26                                                                                                                                      

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

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
               SCOP domains d3knfb_ B: autom         ated matches                                                                                                                             SCOP domains
               CATH domains 3knfB00 B:1-161           [code=3.50.80.10, no name defined]                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.---------..eeeeee..eeeeeee.....hhhhhhhhhhhhhhh.............hhhhh.eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knf B   1 MRVVIQRVKGAILSVR---------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10     |   -     |  30        40        50        60        70        80        90       100       110       120       130       140       150       160 
                                          16        26                                                                                                                                       

Chain C from PDB  Type:PROTEIN  Length:150
 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 d3knfc_ C: automa        ted matches                                                                                                                             SCOP domains
               CATH domains 3knfC00 C:1-160          [code=3.50.80.10, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..--------..eeeeee..eeeeeee.....hhhhhhhhhhhhhhh.....--.....hhhhhh.eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhhhhh.eee......eeeeeeeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knf C   1 MRVVIQRVKGAILSVRK--------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNN--KTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10      |  -     |  30        40        50        60      | 70        80        90       100       110       120       130       140       150       160
                                           17       26                                       67 70                                                                                          

Chain D from PDB  Type:PROTEIN  Length:154
 aligned with Q8IIS0_PLAF7 | Q8IIS0 from UniProtKB/TrEMBL  Length:164

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
               SCOP domains d3knfd_ D: automat       ed matches                                                                                                                               SCOP domains
               CATH domains 3knfD00 D:1-161  [       code=3.50.80.10, no name defined]                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee..-------.eeeeeee..eeeeeee.....hhhhhhhhhhhhhhheeeee..eeeeee......eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knf D   1 MRVVIQRVKGAILSVRKE-------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10       | -     |  30        40        50        60        70        80        90       100       110       120       130       140       150       160 
                                            18      26                                                                                                                                       

Chain E from PDB  Type:PROTEIN  Length:150
 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 d3knfe_ E: autom          ated matches                                                                                                                           SCOP domains
               CATH domains 3knfE00 E:1-160            [code=3.50.80.10, no name defined]                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee.----------.eeeeeeeee..eeee.....hhhhhhhhhhhhhhh....................eeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....ee.......eeeeeeeeeeee..ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knf E   1 MRVVIQRVKGAILSVR----------LEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDI 160
                                    10     |   -      | 30        40        50        60        70        80        90       100       110       120       130       140       150       160
                                          16         27                                                                                                                                     

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

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q8IIS0_PLAF7     1 MRVVIQRVKGAILSVRKENIGENEKELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
               SCOP domains d3knff_ F: autom         ated matches                                                                                                                             SCOP domains
               CATH domains 3knfF00 F:1-161           [code=3.50.80.10, no name defined]                                                                                                      CATH domains
           Pfam domains (1) -Tyr_Deacylase-3         knfF01 F:2-157                                                                                                                      ---- Pfam domains (1)
           Pfam domains (2) -Tyr_Deacylase-3         knfF02 F:2-157                                                                                                                      ---- Pfam domains (2)
           Pfam domains (3) -Tyr_Deacylase-3         knfF03 F:2-157                                                                                                                      ---- Pfam domains (3)
           Pfam domains (4) -Tyr_Deacylase-3         knfF04 F:2-157                                                                                                                      ---- Pfam domains (4)
           Pfam domains (5) -Tyr_Deacylase-3         knfF05 F:2-157                                                                                                                      ---- Pfam domains (5)
           Pfam domains (6) -Tyr_Deacylase-3         knfF06 F:2-157                                                                                                                      ---- Pfam domains (6)
         Sec.struct. author .eeeeeeeeeeeeee.---------..ee......eeeeeee.....hhhhhhhhhhhhhhh..eee..eeeee.hhhhh.eeeeee.hhhhh..............hhhhhhhhhhhhhhhhhhhh....eee......eeeeeeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3knf F   1 MRVVIQRVKGAILSVR---------ELEIISEIKNGLICFLGIHKNDTWEDALYIIRKCLNLRLWNNDNKTWDKNVKDLNYELLIVSQFTLFGNTKKGNKPDFHLAKEPNEALIFYNKIIDEFKKQYNDDKIKIGKFGNYMNIDVTNDGPVTIYIDTHDIN 161
                                    10     |   -     |  30        40        50        60        70        80        90       100       110       120       130       140       150       160 
                                          16        26                                                                                                                                       

   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, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit

(-) 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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  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 | Q8IIS03knp 3ko3 3ko4 3ko5 3ko7 3ko9 3kob 3koc 3kod 3lmt 3lmu 3lmv 4nbi 4nbj 5j61

(-) Related Entries Specified in the PDB File

1j7g 1jke 1tc5 2dbo 3knp 3ko3 3ko4 3ko5 3ko7 3ko9 3kob 3koc 3kod