Crystal structure of the 5'-deoxynucleotidase YfbR mutant E72A complexed with Co(2+) and TMP

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Structural insight into the mechanism of substrate specificity and catalytic activity of an HD-domain phosphohydrolase: the 5'-deoxyribonucleotidase YfbR from Escherichia coli.

Zimmerman, M.D.Proudfoot, M.Yakunin, A.Minor, W.

(2008) J Mol Biol 378: 215-226

  • DOI: https://doi.org/10.1016/j.jmb.2008.02.036
  • Primary Citation of Related Structures:  
    2PAQ, 2PAR, 2PAU

  • PubMed Abstract: 

    HD-domain phosphohydrolases have nucleotidase and phosphodiesterase activities and play important roles in the metabolism of nucleotides and in signaling. We present three 2.1-A-resolution crystal structures (one in the free state and two complexed with natural substrates) of an HD-domain phosphohydrolase, the Escherichia coli 5'-nucleotidase YfbR. The free-state structure of YfbR contains a large cavity accommodating the metal-coordinating HD motif (H33, H68, D69, and D137) and other conserved residues (R18, E72, and D77). Alanine scanning mutagenesis confirms that these residues are important for activity. Two structures of the catalytically inactive mutant E72A complexed with Co(2+) and either thymidine-5'-monophosphate or 2'-deoxyriboadenosine-5'-monophosphate disclose the novel binding mode of deoxyribonucleotides in the active site. Residue R18 stabilizes the phosphate on the Co(2+), and residue D77 forms a strong hydrogen bond critical for binding the ribose. The indole side chain of W19 is located close to the 2'-carbon atom of the deoxyribose moiety and is proposed to act as the selectivity switch for deoxyribonucleotide, which is supported by comparison to YfdR, another 5'-nucleotidase in E. coli. The nucleotide bases of both deoxyriboadenosine-5'-monophosphate and thymidine-5'-monophosphate make no specific hydrogen bonds with the protein, explaining the lack of nucleotide base selectivity. The YfbR E72A substrate complex structures also suggest a plausible single-step nucleophilic substitution mechanism. This is the first proposed molecular mechanism for an HD-domain phosphohydrolase based directly on substrate-bound crystal structures.

  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Ave, Charlottesville, VA 22908, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-deoxynucleotidase YfbR
A, B
201Escherichia coli K-12Mutation(s): 1 
Gene Names: yfbRb2291JW2288
Find proteins for P76491 (Escherichia coli (strain K12))
Explore P76491 
Go to UniProtKB:  P76491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76491
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.136α = 90
b = 136.136β = 90
c = 55.418γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2022-04-13
    Changes: Database references, Structure summary
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description