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(-) Description

Title :  THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX WITH SUBSTRATE ANALOGUE DUPNPP
 
Authors :  G. R. Hemsworth, O. V. Moroz, M. J. Fogg, B. Scott, C. Bosch-Navarrete, D. Gonzalez-Pacanowska, K. S. Wilson
Date :  25 Feb 11  (Deposition) - 16 Mar 11  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Leishmaniasis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. R. Hemsworth, O. V. Moroz, M. J. Fogg, B. Scott, C. Bosch-Navarrete, D. Gonzalez-Pacanowska, K. S. Wilson
The Crystal Structure Of The Leishmania Major Deoxyuridine Triphosphate Nucleotidohydrolase In Complex With Nucleotide Analogues, Dump, And Deoxyuridine.
J. Biol. Chem. V. 286 16470 2011
PubMed-ID: 21454646  |  Reference-DOI: 10.1074/JBC.M111.224873

(-) Compounds

Molecule 1 - DUTPASE
    Chains: A
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-YSBLLIC3C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Strain: 252
    Synonym: DEOXYURIDINE TRIPHOSPHATASE (DUTP DIPHOSPHATASE), DEOXYURIDINE TRIPHOSPHATE NUCLEOTIDOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2DUP1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DUP2Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:21 , LEU A:24 , ASN A:25 , ILE A:28 , TRP A:41 , GLU A:48 , GLU A:51 , LYS A:59 , TRP A:60 , TRP A:61 , ASP A:79 , HIS A:82 , PHE A:83 , LYS A:179 , ASN A:183 , ARG A:186 , TYR A:191 , LYS A:198 , ASN A:206 , CA A:1266 , CA A:1267 , HOH A:2011 , HOH A:2026 , HOH A:2054 , HOH A:2055BINDING SITE FOR RESIDUE DUP A1265
2AC2SOFTWAREGLU A:48 , GLU A:51 , DUP A:1265 , CA A:1267 , HOH A:2011BINDING SITE FOR RESIDUE CA A1266
3AC3SOFTWAREGLU A:48 , GLU A:51 , GLU A:76 , ASP A:79 , DUP A:1265 , CA A:1266 , HOH A:2026BINDING SITE FOR RESIDUE CA A1267

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YAY)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:130 -Pro A:131

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YAY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YAY)

(-) Exons   (0, 0)

(no "Exon" information available for 2YAY)

(-) 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:257
 aligned with O15826_LEIMA | O15826 from UniProtKB/TrEMBL  Length:268

    Alignment length:257
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       
         O15826_LEIMA     8 NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
               SCOP domains d2yaya_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----dUTPase_2-2yayA01 A:13-191                                                                                                                                                         ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhh.........ee......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.........ee..ee.hhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yay A   8 NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257
   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, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YAY)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: MazG (25)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (O15826_LEIMA | O15826)
molecular function
    GO:0004170    dUTP diphosphatase activity    Catalysis of the reaction: dUTP + H2O = dUMP + diphosphate.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  3.6.1.23
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 Related Entries

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

UniProtKB/TrEMBL
        O15826_LEIMA | O15826: 2cje 2yaz 2yb0

(-) Related Entries Specified in the PDB File

2cic THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPASE WITH SUBSTRATE ANALOGUE DUPNHPP
2cje THE CRYSTAL STRUCTURE OF A COMPLEX OF LEISHMANIA MAJOR DUTPASE WITH SUBSTRATE ANALOGUE DUPNHP
2yaz THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX DUMP
2yb0 THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX DEOXYURIDINE