5NZ2

Twist and induce: Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80 dUTPase. D95E mutant from dUTPase 80alpha phage.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80 alpha dUTPase.

Alite, C.Humphrey, S.Donderis, J.Maiques, E.Ciges-Tomas, J.R.Penades, J.R.Marina, A.

(2017) Sci Rep 7: 11234-11234

  • DOI: https://doi.org/10.1038/s41598-017-11234-9
  • Primary Citation of Related Structures:  
    5NYZ, 5NZ2

  • PubMed Abstract: 

    The trimeric staphylococcal phage-encoded dUTPases (Duts) are signalling molecules that induce the cycle of some Staphylococcal pathogenicity islands (SaPIs) by binding to the SaPI-encoded Stl repressor. To perform this regulatory role, these Duts require an extra motif VI, as well as the Dut conserved motifs IV and V. While the apo form of Dut is required for the interaction with the Stl repressor, usually only those Duts with normal enzymatic activity can induce the SaPI cycle. To understand the link between the enzymatic activities and inducing capacities of the Dut protein, we analysed the structural, biochemical and physiological characteristics of the Dut80α D95E mutant, which loses the SaPI cycle induction capacity despite retaining enzymatic activity. Asp95 is located at the threefold central channel of the trimeric Dut where it chelates a divalent ion. Here, using state-of-the-art techniques, we demonstrate that D95E mutation has an epistatic effect on the motifs involved in Stl binding. Thus, ion binding in the central channel correlates with the capacity of motif V to twist and order in the SaPI-inducing disposition, while the tip of motif VI is disturbed. These alterations in turn reduce the affinity for the Stl repressor and the capacity to induce the SaPI cycle.


  • Organizational Affiliation

    Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER), Jaume Roig 11, 46010, Valencia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DUTPase170Dubowvirus dv80alphaMutation(s): 1 
EC: 3.6.1.23
UniProt
Find proteins for A4ZF98 (Staphylococcus phage 80alpha)
Explore A4ZF98 
Go to UniProtKB:  A4ZF98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4ZF98
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.192α = 90
b = 87.192β = 90
c = 87.192γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBES2014-068617
Spanish Ministry of Economy and CompetitivenessSpainBIO2013-42619-P

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description