2XY3

Structure of the Bacillus subtilis prophage dUTPase with dUpNHpp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The Structure of Bacillus Subtilis Sp Beta Prophage Dutpase and its Complexes with Two Nucleotides

Garcia-Nafria, J.Harkiolaki, M.Persson, R.Fogg, M.J.Wilson, K.S.

(2011) Acta Crystallogr D Biol Crystallogr 67: 167

  • DOI: https://doi.org/10.1107/S0907444911003234
  • Primary Citation of Related Structures:  
    2XX6, 2XY3, 2Y1T

  • PubMed Abstract: 

    dUTPases are housekeeping enzymes which catalyse the hydrolysis of dUTP to dUMP in an ion-dependent manner. Bacillus subtilis has both a genomic and an SPβ prophage homotrimeric dUTPase. Here, structure determination of the prophage apoenzyme and of its complexes with dUDP and dUpNHpp-Mg(2+) is described at 1.75, 1.9 and 2.55 Å resolution, respectively. The C-terminal extension, which carries the conserved motif V, is disordered in all three structures. Unlike all other trimeric dUTPases for which structures are available, with the exception of the Bacillus genomic enzyme, the aromatic residue covering the uridine and acting as the Phe-lid is close to motif III in the sequence rather than in motif V. This is in spite of the presence of an aromatic amino acid at the usual Phe-lid position in motif V. The alternative position of the Phe-lid requires a reconsideration of its role in the catalytic cycle of the enzyme. In the dUpNHpp-Mg(2+) complex a water can be seen at the position expected for nucleophilic attack on the α-phosphate, in spite of motif V being disordered. Differences in the active site between the free enzyme and the dUDP and dUpNHpp-Mg(2+) complexes shows that the triphosphate moiety needs to be in the gauche conformation to trigger the conformational changes that can be seen in both B. subtilis dUTPases.


  • Organizational Affiliation

    Department of Chemistry, University of York, York, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
A, B, C, D, E
A, B, C, D, E, F
142Bacillus subtilisMutation(s): 0 
EC: 3.6.1.23
UniProt
Find proteins for O34919 (Bacillus subtilis (strain 168))
Explore O34919 
Go to UniProtKB:  O34919
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34919
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DUP
Query on DUP

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
I [auth C]
K [auth D]
L [auth E]
G [auth A],
H [auth B],
I [auth C],
K [auth D],
L [auth E],
N [auth F]
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
C9 H16 N3 O13 P3
XZLLMTSKYYYJLH-SHYZEUOFSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth C],
M [auth E],
O [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.474α = 90
b = 98.4β = 90
c = 97.993γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description