Convergent evolution involving dimeric and trimeric dUTPases in signalling.

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization.

Donderis, J.Bowring, J.Maiques, E.Ciges-Tomas, J.R.Alite, C.Mehmedov, I.Tormo-Mas, M.A.Penades, J.R.Marina, A.

(2017) PLoS Pathog 13: e1006581-e1006581

  • DOI: https://doi.org/10.1371/journal.ppat.1006581
  • Primary Citation of Related Structures:  
    5MYD, 5MYF, 5MYI

  • PubMed Abstract: 

    The dUTPase (Dut) enzymes, encoded by almost all free-living organisms and some viruses, prevent the misincorporation of uracil into DNA. We previously proposed that trimeric Duts are regulatory proteins involved in different cellular processes; including the phage-mediated transfer of the Staphylococcus aureus pathogenicity island SaPIbov1. Recently, it has been shown that the structurally unrelated dimeric Dut encoded by phage ϕNM1 is similarly able to mobilize SaPIbov1, suggesting dimeric Duts could also be regulatory proteins. How this is accomplished remains unsolved. Here, using in vivo, biochemical and structural approaches, we provide insights into the signaling mechanism used by the dimeric Duts to induce the SaPIbov1 cycle. As reported for the trimeric Duts, dimeric Duts contain an extremely variable region, here named domain VI, which is involved in the regulatory capacity of these enzymes. Remarkably, our results also show that the dimeric Dut signaling mechanism is modulated by dUTP, as with the trimeric Duts. Overall, our results demonstrate that although unrelated both in sequence and structure, dimeric and trimeric Duts control SaPI transfer by analogous mechanisms, representing a fascinating example of convergent evolution. This conserved mode of action highlights the biological significance of Duts as regulatory molecules.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
207Staphylococcus sp. HMSC068C09Mutation(s): 0 
Gene Names: HMPREF2930_08375
Find proteins for A0A2D0TC86 (Staphylococcus sp. HMSC068C09)
Explore A0A2D0TC86 
Go to UniProtKB:  A0A2D0TC86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2D0TC86
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DUP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
N [auth D]
C9 H16 N3 O13 P3
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
I [auth B]
J [auth B]
L [auth C]
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
O [auth D],
P [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.89α = 90
b = 81.44β = 106.92
c = 81.53γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2013-42619-P
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-78571-P
Valencian GovernmentSpainPrometeo II/2014/029
Medical Research Council (United Kingdom)United KingdomMR/M003876/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N002873/1
European Research CouncilERC-ADG-2014

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Refinement description