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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI DUTPASE WITH DUPNP, CA2+ AND NA+
 
Authors :  G. R. Hemsworth, D. Gonzalez-Pacanowska, K. S. Wilson
Date :  03 Feb 12  (Deposition) - 07 Aug 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  All Alpha Ntp Pyrophosphohydrolase, All Alpha Ntp Pyrophosphatase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. R. Hemsworth, D. Gonzalez-Pacanowska, K. S. Wilson
On The Catalytic Mechanism Of Dimeric Dutpases.
Biochem. J. V. 456 81 2013
PubMed-ID: 24001052  |  Reference-DOI: 10.1042/BJ20130796

(-) Compounds

Molecule 1 - DEOXYURIDINE TRIPHOSPHATASE
    Chains: A, B
    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
    Gene: TB927.7.5160
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Strain: 427
    Synonym: DEOXYURIDINE TRIPHOSPHATE NUCLEOTIDOHYDROLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2DUN2Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-DIPHOSPHATE
3NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:21 , LEU A:24 , ASN A:25 , TRP A:41 , GLU A:48 , GLU A:51 , ASP A:79 , HIS A:82 , PHE A:83 , LYS A:208 , ASN A:212 , ARG A:215 , TYR A:220 , LYS A:227 , ASN A:235 , CA A:302 , CA A:303 , HOH A:403 , HOH A:405 , HOH A:409 , HOH A:440 , LYS B:59 , TRP B:60 , TRP B:61BINDING SITE FOR RESIDUE DUN A 301
2AC2SOFTWAREGLU A:48 , GLU A:51 , DUN A:301 , CA A:303 , HOH A:401 , HOH A:402BINDING SITE FOR RESIDUE CA A 302
3AC3SOFTWAREGLU A:48 , GLU A:51 , GLU A:76 , ASP A:79 , DUN A:301 , CA A:302 , HOH A:403BINDING SITE FOR RESIDUE CA A 303
4AC4SOFTWAREGLU A:51 , GLU A:76 , HOH A:403 , HOH A:405 , HOH A:406 , HOH A:407BINDING SITE FOR RESIDUE NA A 304
5AC5SOFTWARELYS A:59 , TRP A:60 , TRP A:61 , GLN B:21 , LEU B:24 , ASN B:25 , TRP B:41 , GLU B:48 , GLU B:51 , ASP B:79 , HIS B:82 , PHE B:83 , LYS B:208 , ASN B:212 , ARG B:215 , TYR B:220 , LYS B:227 , ASN B:235 , CA B:302 , CA B:303 , HOH B:402 , HOH B:471BINDING SITE FOR RESIDUE DUN B 301
6AC6SOFTWAREHOH A:404 , GLU B:48 , GLU B:51 , DUN B:301 , CA B:303 , HOH B:401BINDING SITE FOR RESIDUE CA B 302
7AC7SOFTWAREGLU B:48 , GLU B:51 , GLU B:76 , ASP B:79 , DUN B:301 , CA B:302 , HOH B:402BINDING SITE FOR RESIDUE CA B 303
8AC8SOFTWAREGLU B:51 , GLU B:76 , HOH B:402 , HOH B:432 , HOH B:490BINDING SITE FOR RESIDUE NA B 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DK4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:159 -Pro A:160
2Phe B:159 -Pro B:160

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DK4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DK4)

(-) Exons   (0, 0)

(no "Exon" information available for 4DK4)

(-) 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:218
 aligned with Q57ZH3_TRYB2 | Q57ZH3 from UniProtKB/TrEMBL  Length:287

    Alignment length:279
                                    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       267       277         
         Q57ZH3_TRYB2     8 SLSPLILRSLAELQDGLNTVVDKNWRQLRRPGDWSLAITMEAAELLDSYPWKWWKNVKAQPDLQNVKIELTDILHFSLSGAMQVSDENSGAVHKAEAGSNGESGKHWCYFDQPRALPAAGGAEYVACVETPGSSLSAPVSADECDLADFMFFPLSDTNNALASFQNIIRLASLQRFQLVTSAVIAAADDIGFNLVAYYVAKHTLNGIRQMKGYKDGTYVKVQKGVEDNELLHGCISPFSLDDVTNEGNYKTKWDDIMHRVYDAFGTPKEERLNIGHWLK 286
               SCOP domains d4dk4a_ A: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhhh-------------------------------------------------------------.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.........ee..ee...hhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhh.hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dk4 A   8 SLSPLILRSLAELQDGLNTVVDKNWRQLRRPGDWSLAITMEAAELLDSYPWKWWKNVKAQPDLQNVKIELTDILHFSLSGAMQVS-------------------------------------------------------------ADFMFFPLSDTNNALASFQNIIRLASLQRFQLVTSAVIAAADDIGFNLVAYYVAKHTLNGIRQMKGYKDGTYVKVQKGVEDNELLHGCISPFSLDDVTNEGNYKTKWDDIMHRVYDAFGTPKEERLNIGHWLK 286
                                    17        27        37        47        57        67        77        87    |    -         -         -         -         -         -      |157       167       177       187       197       207       217       227       237       247       257       267       277         
                                                                                                               92                                                           154                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with Q57ZH3_TRYB2 | Q57ZH3 from UniProtKB/TrEMBL  Length:287

    Alignment length:277
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       
         Q57ZH3_TRYB2     9 LSPLILRSLAELQDGLNTVVDKNWRQLRRPGDWSLAITMEAAELLDSYPWKWWKNVKAQPDLQNVKIELTDILHFSLSGAMQVSDENSGAVHKAEAGSNGESGKHWCYFDQPRALPAAGGAEYVACVETPGSSLSAPVSADECDLADFMFFPLSDTNNALASFQNIIRLASLQRFQLVTSAVIAAADDIGFNLVAYYVAKHTLNGIRQMKGYKDGTYVKVQKGVEDNELLHGCISPFSLDDVTNEGNYKTKWDDIMHRVYDAFGTPKEERLNIGHWL 285
               SCOP domains d4dk4b_ B: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh------------------------------------------------------------hhhhh......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhh..hhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dk4 B   9 LSPLILRSLAELQDGLNTVVDKNWRQLRRPGDWSLAITMEAAELLDSYPWKWWKNVKAQPDLQNVKIELTDILHFSLSGAMQV------------------------------------------------------------DLADFMFFPLSDTNNALASFQNIIRLASLQRFQLVTSAVIAAADDIGFNLVAYYVAKHTLNGIRQMKGYKDGTYVKVQKGVEDNELLHGCISPFSLDDVTNEGNYKTKWDDIMHRVYDAFGTPKEERLNIGHWL 285
                                    18        28        38        48        58        68        78        88  |      -         -         -         -         -         -   |   158       168       178       188       198       208       218       228       238       248       258       268       278       
                                                                                                             91                                                          152
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DK4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DK4)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q57ZH3_TRYB2 | Q57ZH3)
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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  Q57ZH3_TRYB2 | Q57ZH3
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 Related Entries

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

UniProtKB/TrEMBL
        Q57ZH3_TRYB2 | Q57ZH3: 4dk2 4dkb 4dl8 4dlc

(-) Related Entries Specified in the PDB File

4dk2 4dkb 4dl8 4dlc