4WJY

Esherichia coli nitrite reductase NrfA H264N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 3.0 of the entry. See complete history

Literature

Resolution of key roles for the distal pocket histidine in cytochrome C nitrite reductases.

Lockwood, C.W.Burlat, B.Cheesman, M.R.Kern, M.Simon, J.Clarke, T.A.Richardson, D.J.Butt, J.N.

(2015) J.Am.Chem.Soc. 137: 3059-3068

  • DOI: 10.1021/ja512941j

  • PubMed Abstract: 
  • Cytochrome c nitrite reductases perform a key step in the biogeochemical N-cycle by catalyzing the six-electron reduction of nitrite to ammonium. These multiheme cytochromes contain a number of His/His ligated c-hemes for electron transfer and a stru ...

    Cytochrome c nitrite reductases perform a key step in the biogeochemical N-cycle by catalyzing the six-electron reduction of nitrite to ammonium. These multiheme cytochromes contain a number of His/His ligated c-hemes for electron transfer and a structurally differentiated heme that provides the catalytic center. The catalytic heme has proximal ligation from lysine, or histidine, and an exchangeable distal ligand bound within a pocket that includes a conserved histidine. Here we describe properties of a penta-heme cytochrome c nitrite reductase in which the distal His has been substituted by Asn. The variant is unable to catalyze nitrite reduction despite retaining the ability to reduce a proposed intermediate in that process, namely, hydroxylamine. A combination of electrochemical, structural and spectroscopic studies reveals that the variant enzyme simultaneously binds nitrite and electrons at the catalytic heme. As a consequence the distal His is proposed to play a key role in orienting the nitrite for N-O bond cleavage. The electrochemical experiments also reveal that the distal His facilitates rapid nitrite binding to the catalytic heme of the native enzyme. Finally it is noted that the thermodynamic descriptions of nitrite- and electron-binding to the active site of the variant enzyme are modulated by the prevailing oxidation states of the His/His ligated hemes. This behavior is likely to be displayed by other multicentered redox enzymes such that there are wide implications for considering the determinants of catalytic activity in this important and varied group of oxidoreductases.


    Organizational Affiliation

    Centre for Molecular and Structural Biochemistry, School of Chemistry and ‡School of Biological Sciences, University of East Anglia , Norwich Research Park, Norwich, NR4 7TJ, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-552
A, B
452Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: nrfA
EC: 1.7.2.2
Find proteins for P0ABK9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABK9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HEC
Query on HEC

Download SDF File 
Download CCD File 
A, B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.240α = 90.00
b = 89.490β = 90.00
c = 274.720γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
REFMACrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomB18695

Revision History 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2015-03-18
    Type: Database references
  • Version 2.0: 2017-08-30
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations
  • Version 3.0: 2019-01-23
    Type: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary