Crystal structure of pentaerythritol tetranitrate reductase (PETNR) mutant I107A

  • Classification: FLAVOPROTEIN
  • Organism(s): Enterobacter cloacae
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2018-05-10 Released: 2019-03-20 
  • Deposition Author(s): Levy, C.W.
  • Funding Organization(s): Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.141 

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Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes.

Iorgu, A.I.Baxter, N.J.Cliff, M.J.Levy, C.Waltho, J.P.Hay, S.Scrutton, N.S.

(2018) ACS Catal 8: 11589-11599

  • DOI: https://doi.org/10.1021/acscatal.8b02810
  • Primary Citation of Related Structures:  
    6GI7, 6GI8, 6GI9, 6GIA

  • PubMed Abstract: 

    Many enzymes that catalyze hydride transfer reactions work via a mechanism dominated by quantum mechanical tunneling. The involvement of fast vibrational modes of the reactive complex is often inferred in these reactions, as in the case of the NAD(P)H-dependent pentaerythritol tetranitrate reductase (PETNR). Herein, we interrogated the H-transfer mechanism in PETNR by designing conservative (L25I and I107L) and side chain shortening (L25A and I107A) PETNR variants and using a combination of experimental approaches (stopped-flow rapid kinetics, X-ray crystallography, isotope/temperature dependence studies of H-transfer and NMR spectroscopy). X-ray data show subtle changes in the local environment of the targeted side chains but no major structural perturbation caused by mutagenesis of these two second sphere active site residues. However, temperature dependence studies of H-transfer revealed a coenzyme-specific and complex thermodynamic equilibrium between different reactive configurations in PETNR-coenzyme complexes. We find that mutagenesis of these second sphere "noncatalytic" residues affects differently the reactivity of PETNR with NADPH and NADH coenzymes. We attribute this to subtle, dynamic structural changes in the PETNR active site, the effects of which impact differently in the nonequivalent reactive geometries of PETNR-NADH and PETNR-NADPH complexes. This inference is confirmed through changes observed in the NMR chemical shift data for PETNR complexes with unreactive 1,4,5,6-tetrahydro-NAD(P) analogues. We show that H-transfer rates can (to some extent) be buffered through entropy-enthalpy compensation, but that use of integrated experimental tools reveals hidden complexities that implicate a role for dynamics in this relatively simple H-transfer reaction. Similar approaches are likely to be informative in other enzymes to understand the relative importance of (distal) hydrophobic side chains and dynamics in controlling the rates of enzymatic H-transfer.

  • Organizational Affiliation

    Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pentaerythritol tetranitrate reductase373Enterobacter cloacaeMutation(s): 1 
Gene Names: onr
Find proteins for P71278 (Enterobacter cloacae)
Explore P71278 
Go to UniProtKB:  P71278
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71278
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FMN

Download Ideal Coordinates CCD File 
C17 H21 N4 O9 P
Query on ACT

Download Ideal Coordinates CCD File 
C2 H3 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.872α = 90
b = 69.139β = 90
c = 88.894γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2019-03-20 
  • Deposition Author(s): Levy, C.W.

Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomJ020192
Biotechnology and Biological Sciences Research CouncilUnited KingdomM007065
Biotechnology and Biological Sciences Research CouncilUnited KingdomH021523

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description