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(-) Description

Title :  THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX DEOXYURIDINE
 
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 :  2.28
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  D,E  (1x)
Keywords :  Hydrolase (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, B, D, E
    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
    Expression System Vector Type: PLASMID
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Strain: 252
    Synonym: DEOXYURIDINE TRIPHOSPHATE NUCLEOTIDOHYDROLASE, DEOXYURIDINE TRIPHOSPHATASE, DUTP DIPHOSPHATASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1DUR4Ligand/Ion2'-DEOXYURIDINE
2SO49Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1DUR2Ligand/Ion2'-DEOXYURIDINE
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1DUR2Ligand/Ion2'-DEOXYURIDINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:21 , LEU A:24 , ASN A:25 , ILE A:28 , TRP A:41 , GLU A:48 , ASP A:79 , HIS A:82 , PHE A:83 , ASN A:183 , SO4 A:1267 , HOH A:2029 , TRP B:60 , TRP B:61BINDING SITE FOR RESIDUE DUR A1266
02AC2SOFTWAREARG A:186 , TYR A:191 , LYS A:198 , DUR A:1266 , HOH A:2006 , HOH A:2038 , LYS B:59 , TRP B:61 , LYS B:62BINDING SITE FOR RESIDUE SO4 A1267
03AC3SOFTWARESO4 A:1269 , HOH A:2039 , LYS B:59 , LYS B:62 , ASN B:63BINDING SITE FOR RESIDUE SO4 A1268
04AC4SOFTWAREVAL A:197 , LYS A:198 , VAL A:199 , SO4 A:1268 , LYS B:62BINDING SITE FOR RESIDUE SO4 A1269
05AC5SOFTWARETRP A:60 , TRP A:61 , GLN B:21 , LEU B:24 , ASN B:25 , ILE B:28 , TRP B:41 , ASP B:79 , HIS B:82 , PHE B:83 , ASN B:183 , SO4 B:1267 , HOH B:2015 , HOH B:2018BINDING SITE FOR RESIDUE DUR B1266
06AC6SOFTWARELYS A:59 , TRP A:61 , LYS A:62 , ARG B:186 , TYR B:191 , LYS B:198 , DUR B:1266 , SO4 B:1268 , HOH B:2019BINDING SITE FOR RESIDUE SO4 B1267
07AC7SOFTWARELYS A:59 , LYS A:62 , ASN A:63 , SO4 B:1267BINDING SITE FOR RESIDUE SO4 B1268
08AC8SOFTWAREGLN D:21 , LEU D:24 , ASN D:25 , ILE D:28 , TRP D:41 , ASP D:79 , HIS D:82 , PHE D:83 , ASN D:183 , ARG D:186 , SO4 D:1267 , TRP E:60 , TRP E:61BINDING SITE FOR RESIDUE DUR D1266
09AC9SOFTWAREARG D:186 , TYR D:191 , LYS D:198 , DUR D:1266 , HOH D:2023 , LYS E:59 , TRP E:61 , LYS E:62BINDING SITE FOR RESIDUE SO4 D1267
10BC1SOFTWARELYS E:59 , LYS E:62 , ASN E:63BINDING SITE FOR RESIDUE SO4 D1268
11BC2SOFTWARETRP D:60 , TRP D:61 , GLN E:21 , LEU E:24 , ASN E:25 , ILE E:28 , TRP E:41 , ASP E:79 , HIS E:82 , PHE E:83 , ASN E:183 , SO4 E:1267 , HOH E:2011BINDING SITE FOR RESIDUE DUR E1266
12BC3SOFTWARELYS D:59 , TRP D:61 , LYS D:62 , ARG E:186 , TYR E:191 , LYS E:198 , DUR E:1266 , HOH E:2015BINDING SITE FOR RESIDUE SO4 E1267
13BC4SOFTWARELYS D:59 , LYS D:62 , ASN D:63BINDING SITE FOR RESIDUE SO4 E1268

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YB0)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Phe A:130 -Pro A:131
2Phe B:130 -Pro B:131
3Phe D:130 -Pro D:131
4Phe E:130 -Pro E:131
5Asn E:200 -Asn E:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YB0)

(-) Exons   (0, 0)

(no "Exon" information available for 2YB0)

(-) 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:258
 aligned with O15826_LEIMA | O15826 from UniProtKB/TrEMBL  Length:268

    Alignment length:258
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256        
         O15826_LEIMA     7 ANIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
               SCOP domains d2yb0a_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.........ee..ee.hhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yb0 A   7 ANIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256        


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with O15826_LEIMA | O15826 from UniProtKB/TrEMBL  Length:268

    Alignment length:263
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   
         O15826_LEIMA     2 KRARSANIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
               SCOP domains d2yb0b_ B: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.........ee......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.........ee..ee...hhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yb0 B   2 KRARSANIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261   


Chain D from PDB  Type:PROTEIN  Length:255
 aligned with O15826_LEIMA | O15826 from UniProtKB/TrEMBL  Length:268

    Alignment length:255
                                    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 NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKEN 262
               SCOP domains d2yb0d_ D: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..........ee......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.........ee..ee...hhhhhhhh..........hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yb0 D   8 NIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKEN 262
                                    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     


Chain E from PDB  Type:PROTEIN  Length:264
 aligned with O15826_LEIMA | O15826 from UniProtKB/TrEMBL  Length:268

    Alignment length:264
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
         O15826_LEIMA     1 MKRARSANIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
               SCOP domains d2yb0e_ E: automated matches                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------dUTPase_2-2yb0E01 E:13-191                                                                                                                                                         ------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------dUTPase_2-2yb0E02 E:13-191                                                                                                                                                         ------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------dUTPase_2-2yb0E03 E:13-191                                                                                                                                                         ------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------dUTPase_2-2yb0E04 E:13-191                                                                                                                                                         ------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee......ee...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...............hhhhhhhhh....hhhhh...hhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yb0 E   1 MKRARSANIPGAILHSLAELQDGLNAMIDPSWRAVRSLDNWALAITMESTELLDSYPWKWWKNLNATPDLANVRIELVDIFHFSLSGAMQMRSTPDDEIPAASLKPLKEVMTTFLPAKECTSDPYGFVFFPLTDTQNAIASFRNIIQLANAYRFDVIIECIIYAAEDLGFNLVAYYIAKHTLNCIRQLSGYKDGSYVKVNNGVEDNSLLHNCIKDVSLDEVLDADKYVQAWNSIMANVYEAFQIKESDRKDAERWFALAKENRL 264
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YB0)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: MazG (25)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,D,E   (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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  O15826_LEIMA | O15826
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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 2yay 2yaz

(-) 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
2yay THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX WITH SUBSTRATE ANALOGUE DUPNPP
2yaz THE CRYSTAL STRUCTURE OF LEISHMANIA MAJOR DUTPASE IN COMPLEX DUMP