Crystal structure of a putative NTP pyrophosphohydrolase (Exig_1061) from EXIGUOBACTERIUM SP. 255-15 at 1.78 A resolution

Experimental Data Snapshot

  • Resolution: 1.78 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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This is version 1.4 of the entry. See complete history


Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.

Han, G.W.Elsliger, M.A.Yeates, T.O.Xu, Q.Murzin, A.G.Krishna, S.S.Jaroszewski, L.Abdubek, P.Astakhova, T.Axelrod, H.L.Carlton, D.Chen, C.Chiu, H.J.Clayton, T.Das, D.Deller, M.C.Duan, L.Ernst, D.Feuerhelm, J.Grant, J.C.Grzechnik, A.Jin, K.K.Johnson, H.A.Klock, H.E.Knuth, M.W.Kozbial, P.Kumar, A.Lam, W.W.Marciano, D.McMullan, D.Miller, M.D.Morse, A.T.Nigoghossian, E.Okach, L.Reyes, R.Rife, C.L.Sefcovic, N.Tien, H.J.Trame, C.B.van den Bedem, H.Weekes, D.Hodgson, K.O.Wooley, J.Deacon, A.M.Godzik, A.Lesley, S.A.Wilson, I.A.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1237-1244

  • DOI: https://doi.org/10.1107/S1744309110025534
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of a putative NTPase, YP_001813558.1 from Exiguobacterium sibiricum 255-15 (PF09934, DUF2166) was determined to 1.78 Å resolution. YP_001813558.1 and its homologs (dimeric dUTPases, MazG proteins and HisE-encoded phosphoribosyl ATP pyrophosphohydrolases) form a superfamily of all-α-helical NTP pyrophosphatases. In dimeric dUTPase-like proteins, a central four-helix bundle forms the active site. However, in YP_001813558.1, an unexpected intertwined swapping of two of the helices that compose the conserved helix bundle results in a `linked dimer' that has not previously been observed for this family. Interestingly, despite this novel mode of dimerization, the metal-binding site for divalent cations, such as magnesium, that are essential for NTPase activity is still conserved. Furthermore, the active-site residues that are involved in sugar binding of the NTPs are also conserved when compared with other α-helical NTPases, but those that recognize the nucleotide bases are not conserved, suggesting a different substrate specificity.

  • Organizational Affiliation

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
putative NTP pyrophosphohydrolase171Exiguobacterium sibiricum 255-15Mutation(s): 0 
Gene Names: Exig_1061
Find proteins for B1YMF4 (Exiguobacterium sibiricum (strain DSM 17290 / CIP 109462 / JCM 13490 / 255-15))
Explore B1YMF4 
Go to UniProtKB:  B1YMF4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1YMF4
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.088α = 90
b = 69.043β = 111.81
c = 50.208γ = 90
Software Package:
Software NamePurpose
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-02-01
    Changes: Database references, Derived calculations