NMR Solution Structure of DR0079: An hypothetical Nudix protein from D. radiodurans

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 225 
  • Conformers Submitted: 10 
  • Selection Criteria: ten best structures, in terms of total and NOE energies 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium

Buchko, G.W.Ni, S.Holbrook, S.R.Kennedy, M.A.

(2004) Proteins 56: 28-39

  • DOI: https://doi.org/10.1002/prot.20082
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Using nuclear magnetic resonance (NMR) based methods, including residual dipolar coupling restraints, we have determined the solution structure of the hypothetical Deinococcus radiodurans Nudix protein DR0079 (171 residues, MW = 19.3 kDa). The protein contains eight beta-strands and three alpha-helices organized into three subdomains: an N-terminal beta-sheet (1-34), a central Nudix core (35-140), and a C-terminal helix-turn-helix (141-171). The Nudix core and the C-terminal helix-turn-helix form the fundamental fold common to the Nudix family, a large mixed beta-sheet sandwiched between alpha-helices. The residues that compose the signature Nudix sequence, GX5EX7REUXEEXGU (where U = I, L, or V and X = any amino acid), are contained in a turn-helix-turn motif on the face of the mixed beta-sheet. Chemical shift mapping experiments suggest that DR0079 binds Mg2+. Experiments designed to determine the biological function of the protein indicate that it is not a type I isopentenyl-diphosphate delta-isomerase and that it does not bind alpha,beta-methyleneadenosine 5'-triphosphate (AMPCPP) or guanosine 5'-[beta,gamma-imido]triphosphate (GMPPNP). In this article, the structure of DR0079 is compared to other known Nudix protein structures, a potential substrate-binding surface is proposed, and its possible biological function is discussed.

  • Organizational Affiliation

    Fundamental Sciences, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative Nudix hydrolase DR0079171Deinococcus radioduransMutation(s): 0 
Gene Names: DR0079
EC: 3.6.1
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

  • Method: SOLUTION NMR
  • Conformers Calculated: 225 
  • Conformers Submitted: 10 
  • Selection Criteria: ten best structures, in terms of total and NOE energies 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-12
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations