2PAR

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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Literature

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: 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 ...

    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.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-deoxynucleotidase YfbRA, B201Escherichia coli K-12Mutation(s): 1 
Gene Names: yfbR, b2291, JW2288
EC: 3.1.3.5 (PDB Primary Data), 3.1.3.89 (UniProt)
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TMP
Query on TMP
Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]		THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
E [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
CO
Query on CO
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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