Crystal Structure of DR0079 from Deinococcus radiodurans at 1.9 Angstrom Resolution

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.234 

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Functional and Structural Characterization of DR_0079 from Deinococcus radiodurans, a Novel Nudix Hydrolase with a Preference for Cytosine (Deoxy)ribonucleoside 5'-Di- and Triphosphates.

Buchko, G.W.Litvinova, O.Robinson, H.Yakunin, A.F.Kennedy, M.A.

(2008) Biochemistry 47: 6571-6582

  • DOI: https://doi.org/10.1021/bi800099d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The genome of the extremely radiation resistant bacterium Deinococcus radiodurans encodes 21 Nudix hydrolases, of which only two have been characterized in detail. Here we report the activity and crystal structure for DR_0079, the first Nudix hydrolase observed to have a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP). After CDP and CTP, the next most preferred substrates for DR_0079, with a relative activity of <50%, were the corresponding deoxyribose nucleotides, dCDP and dCTP. Hydrolase activity at the site of the phosphodiester bond was corroborated using (31)P NMR spectroscopy to follow the phosphorus resonances for three substrates, CDP, IDP, and CTP, and their hydrolysis products, CMP + P(i), IMP + P(i), and CMP + PP(i), respectively. Nucleophilic substitution at the beta-phosphorus of CDP and CTP was established, using (31)P NMR spectroscopy, by the appearance of an upfield-shifted P(i) resonance and line-broadened PP(i) resonance, respectively, when the hydrolysis was performed in 40% H(2)(18)O-enriched water. The optimal activity for CDP was at pH 9.0-9.5 with the reaction requiring divalent metal cation (Mg(2+) > Mn(2+) > Co(2+)). The biochemical data are discussed with reference to the crystal structure for DR_0079 that was determined in the metal-free form at 1.9 A resolution. The protein contains nine beta-strands, three alpha-helices, and two 3(10)-helices organized into three subdomains: an N-terminal beta-sheet, a central Nudix core, and a C-terminal helix-turn-helix motif. As observed for all known structures of Nudix hydrolases, the alpha-helix of the "Nudix box" is one of two helices that sandwich a "four-strand" mixed beta-sheet. To identify residues potentially involved in metal and substrate binding, NMR chemical shift mapping experiments were performed on (15)N-labeled DR_0079 with the paramagnetic divalent cation Co(2+) and the nonhydrolyzable substrate thymidine 5'-O-(alpha,beta-methylenediphosphate) and the results mapped onto the crystal structure.

  • Organizational Affiliation

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA. garry.buchko@pnl.gov

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative Nudix hydrolase DR_0079
A, B
171Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539Mutation(s): 0 
Gene Names: DR0079
EC: 3.6
Find proteins for Q9RY71 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RY71 
Go to UniProtKB:  Q9RY71
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RY71
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.234 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.019α = 90
b = 156.554β = 90
c = 126.56γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references