4CSP

Structure of the F306C mutant of nitrite reductase from Achromobacter xylosoxidans

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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This is version 1.2 of the entry. See complete history. 


Literature

Impact of Residues Remote from the Catalytic Centre on Enzyme Catalysis of Copper Nitrite Reductase.

Leferink, N.G.H., Antonyuk, S.V., Houwman, J.A., Scrutton, N.S., Eady, R.R., Hasnain, S.S.

(2014) Nat Commun 5: 4395

  • DOI: 10.1038/ncomms5395
  • Primary Citation of Related Structures:  
    4CSZ, 4CSP

  • PubMed Abstract: 

    • Enzyme mechanisms are often probed by structure-informed point mutations and measurement of their effects on enzymatic properties to test mechanistic hypotheses. In many cases, the challenge is to report on complex, often inter-linked elements of cat ...

    Enzyme mechanisms are often probed by structure-informed point mutations and measurement of their effects on enzymatic properties to test mechanistic hypotheses. In many cases, the challenge is to report on complex, often inter-linked elements of catalysis. Evidence for long-range effects on enzyme mechanism resulting from mutations remains sparse, limiting the design/redesign of synthetic catalysts in a predictable way. Here we show that improving the accessibility of the active site pocket of copper nitrite reductase by mutation of a surface-exposed phenylalanine residue (Phe306), located 12 Å away from the catalytic site type-2 Cu (T2Cu), profoundly affects intra-molecular electron transfer, substrate-binding and catalytic activity. Structures and kinetic studies provide an explanation for the lower affinity for the substrate and the alteration of the rate-limiting step in the reaction. Our results demonstrate that distant residues remote from the active site can have marked effects on enzyme catalysis, by driving mechanistic change through relatively minor structural perturbations.

    Organizational Affiliation: 

    Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASEA, F335Achromobacter xylosoxidansMutation(s): 1 
Gene Names: nir, nirK, ERS451415_02178
EC: 1.7.2.1
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans)
Explore O68601 
Go to UniProtKB:  O68601
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.99α = 90
b = 89.99β = 90
c = 289.45γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Derived calculations
  • Version 1.2: 2017-09-13
    Changes: Data collection, Structure summary