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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A COMPLEX OF CAMPYLOBACTER JEJUNI DUTPASE WITH SUBSTRATE ANALOGUE DUPNHP
 
Authors :  O. V. Moroz, M. Harkiolaki, M. Y. Galperin, A. A. Vagin, D. Gonzalez-Pacanowska, K. S. Wilson
Date :  09 Jul 04  (Deposition) - 16 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dutp Pyrophosphatase, Dimeric, Ligand Complex, Magnesium Ions, Pathogen, Drug Target, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. V. Moroz, M. Harkiolaki, M. Y. Galperin, A. A. Vagin, D. Gonzalez-Pacanowska, K. S. Wilson
The Crystal Structure Of A Complex Of Campylobacter Jejuni Dutpase With Substrate Analogue Sheds Light On The Mechanism And Suggests The "Basic Module" For Dimeric D(C/U)Tpases
J. Mol. Biol. V. 342 1583 2004
PubMed-ID: 15364583  |  Reference-DOI: 10.1016/J.JMB.2004.07.050

(-) Compounds

Molecule 1 - DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDE HYDROLASE
    Chains: A, B
    EC Number: 3.6.1.23
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 197
    Synonym: PUTATIVE DUTPASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1DUN2Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE
2MG6Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:46 , GLU A:49 , DUN A:1230 , MG A:1232 , HOH A:2054 , HOH A:2195BINDING SITE FOR RESIDUE MG A1231
2AC2SOFTWAREGLU A:46 , GLU A:49 , GLU A:74 , ASP A:77 , DUN A:1230 , MG A:1231 , MG A:1233 , HOH A:2193BINDING SITE FOR RESIDUE MG A1232
3AC3SOFTWAREGLU A:49 , GLU A:74 , DUN A:1230 , MG A:1232 , HOH A:2091 , HOH A:2177 , HOH A:2193 , HOH A:2194BINDING SITE FOR RESIDUE MG A1233
4AC4SOFTWAREGLU B:46 , GLU B:49 , DUN B:1230 , MG B:1232 , HOH B:2056 , HOH B:2187BINDING SITE FOR RESIDUE MG B1231
5AC5SOFTWAREGLU B:46 , GLU B:49 , GLU B:74 , ASP B:77 , DUN B:1230 , MG B:1231 , MG B:1233 , HOH B:2104BINDING SITE FOR RESIDUE MG B1232
6AC6SOFTWAREGLU B:49 , GLU B:74 , MG B:1232 , HOH B:2104 , HOH B:2105 , HOH B:2171 , HOH B:2188BINDING SITE FOR RESIDUE MG B1233
7AC7SOFTWAREGLN A:14 , LEU A:17 , ASN A:18 , ASN A:22 , TRP A:39 , GLU A:46 , GLU A:49 , ASP A:77 , HIS A:80 , PHE A:81 , LYS A:175 , ASN A:179 , ARG A:182 , TYR A:187 , LYS A:194 , ASN A:202 , MG A:1231 , MG A:1232 , MG A:1233 , HOH A:2054 , HOH A:2161 , HOH A:2193 , HOH A:2194 , HOH A:2195 , LYS B:57 , HIS B:58 , TRP B:59BINDING SITE FOR RESIDUE DUN A1230
8AC8SOFTWARELYS A:57 , HIS A:58 , TRP A:59 , GLN B:14 , LEU B:17 , ASN B:18 , ASN B:22 , TRP B:39 , GLU B:46 , GLU B:49 , ASP B:77 , HIS B:80 , PHE B:81 , LYS B:175 , ASN B:179 , ARG B:182 , TYR B:187 , LYS B:194 , ASN B:202 , MG B:1231 , MG B:1232 , HOH B:2056 , HOH B:2104 , HOH B:2162 , HOH B:2187 , HOH B:2188BINDING SITE FOR RESIDUE DUN B1230

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W2Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W2Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W2Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W2Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1W2Y)

(-) 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:226
 aligned with Q0P8G4_CAMJE | Q0P8G4 from UniProtKB/TrEMBL  Length:229

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
         Q0P8G4_CAMJE     1 MTNIEILENMLKLQQKLNDETNGLNWENGYTKEGKLISWRRCIYMECAELIDSFTWKHWKNISSLTNWENVRIEIVDIWHFILSLLLEEYRDKNNKDFKAIATEVNAVSVFQDFCKEEEYPNEGDIYGILNDIELIIHKCSGFGFNLGELLSTYFTLAIKCGLNLEILYKTYIGKNVLNIFRQNNGYKDGSYKKTWNGKEDNEVLAQILEQELDFDTIYKKLEECYKKA 229
               SCOP domains d1w2ya_ A: Type II deoxyuridine triphosphatase                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh---...hhhhhhhhhhh..hhhhhh......hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.........ee..eehhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w2y A   1 MTNIEILENMLKLQQKLNDETNGLNWENGYTKEGKLISWRRCIYMECAELIDSFTWKHWKNISSLTNWENVRIEIVDIWHFILSLLLEEY---NNKDFKAIATEVNAVSVFQDFCKEEEYPNEGDIYGILNDIELIIHKCSGFGFNLGELLSTYFTLAIKCGLNLEILYKTYIGKNVLNIFRQNNGYKDGSYKKTWNGKEDNEVLAQILEQELDFDTIYKKLEECYKKA 229
                                    10        20        30        40        50        60        70        80        90   |   100       110       120       130       140       150       160       170       180       190       200       210       220         
                                                                                                                    90  94                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with Q0P8G4_CAMJE | Q0P8G4 from UniProtKB/TrEMBL  Length:229

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
         Q0P8G4_CAMJE     1 MTNIEILENMLKLQQKLNDETNGLNWENGYTKEGKLISWRRCIYMECAELIDSFTWKHWKNISSLTNWENVRIEIVDIWHFILSLLLEEYRDKNNKDFKAIATEVNAVSVFQDFCKEEEYPNEGDIYGILNDIELIIHKCSGFGFNLGELLSTYFTLAIKCGLNLEILYKTYIGKNVLNIFRQNNGYKDGSYKKTWNGKEDNEVLAQILEQELDFDTIYKKLEECYKKA 229
               SCOP domains d1w2yb_ B: Type II deoxyuridine triphosphatase                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----dUTPase_2-1w2yB01 B:6-187                                                                                                                                                             ------------------------     ------------- Pfam domains (1)
           Pfam domains (2) -----dUTPase_2-1w2yB02 B:6-187                                                                                                                                                             ------------------------     ------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh--------hhhhhhhhhhhhhhhhhhh.-------.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.........ee..eehhhhhhhhhh.-----hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w2y B   1 MTNIEILENMLKLQQKLNDETNGLNWENGYTKEGKLISWRRCIYMECAELIDSFTWKHWKNISSLTNWENVRIEIVDIWHFILSLLLE--------DFKAIATEVNAVSVFQDFCK-------GDIYGILNDIELIIHKCSGFGFNLGELLSTYFTLAIKCGLNLEILYKTYIGKNVLNIFRQNNGYKDGSYKKTWNGKEDNEVLAQILEQ-----TIYKKLEECYKKA 229
                                    10        20        30        40        50        60        70        80       | -      |100       110     |   -   |   130       140       150       160       170       180       190       200       210|     |220         
                                                                                                                  88       97                116     124                                                                                    211   217
   Legend:   → Mismatch (orange background)
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    → 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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1W2Y)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: MazG (25)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q0P8G4_CAMJE | Q0P8G4)
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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        Q0P8G4_CAMJE | Q0P8G4: 2cic

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