2Y1T

Bacillus subtilis prophage dUTPase in complex with dUDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.,Sect.D 67: 167

  • DOI: 10.1107/S0907444911003234
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPBC2 PROPHAGE-DERIVED DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE YOSS
A, B, C, D, E, F
142Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yosS (yojU)
EC: 3.6.1.23
Find proteins for O34919 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34919
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUD
Query on DUD

Download SDF File 
Download CCD File 
B, C, D, E
DEOXYURIDINE-5'-DIPHOSPHATE
C9 H14 N2 O11 P2
QHWZTVCCBMIIKE-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.140 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 99.515α = 90.00
b = 99.338β = 90.00
c = 99.306γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance