2E81

Cytochrome c Nitrite Reductase from Wolinella succinogenes with bound intermediate hydroxylamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Mechanism of the six-electron reduction of nitrite to ammonia by cytochrome c nitrite reductase

Einsle, O.Messerschmidt, A.Huber, R.Kroneck, P.M.H.Neese, F.

(2002) J.Am.Chem.Soc. 124: 11737-11745

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytochrome c nitrite reductase catalyzes the six-electron reduction of nitrite to ammonia without the release of potential reaction intermediates, such as NO or hydroxylamine. On the basis of the crystallographic observation of reaction intermediates ...

    Cytochrome c nitrite reductase catalyzes the six-electron reduction of nitrite to ammonia without the release of potential reaction intermediates, such as NO or hydroxylamine. On the basis of the crystallographic observation of reaction intermediates and of density functional calculations, we present a working hypothesis for the reaction mechanism of this multiheme enzyme which carries a novel lysine-coordinated heme group (Fe-Lys). It is proposed that nitrite reduction starts with a heterolytic cleavage of the N-O bond which is facilitated by a pronounced back-bonding interaction of nitrite coordinated through nitrogen to the reduced (Fe(II)) but not the oxidized (Fe(III)) active site iron. This step leads to the formation of an [FeNO](6) species and a water molecule and is further facilitated by a hydrogen bonding network that induces an electronic asymmetry in the nitrite molecule that weakens one N-O bond and strengthens the other. Subsequently, two rapid one-electron reductions lead to an [FeNO](8) form and, by protonation, to an Fe(II)-HNO adduct. Hereafter, hydroxylamine will be formed by a consecutive two-electron two-proton step which is dehydrated in the final two-electron reduction step to give ammonia and an additional water molecule. A single electron reduction of the active site closes the catalytic cycle.


    Related Citations: 
    • Structure of cytochrome c nitrite reductase
      Einsle, O.,Messerschmidt, A.,Stach, P.,Bourenkov, G.P.,Bartunik, H.D.,Huber, R.,Kroneck, P.M.H.
      (1999) Nature 400: 476
    • Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and heme-packing motifs
      Einsle, O.,Stach, P.,Messerschmidt, A.,Simon, J.,Kroeger, A.,Huber, R.,Kroneck, P.M.H.
      (2000) J.Biol.Chem. 275: 39608


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Abt. Strukturforschung, Am Klopferspitz 18a, 82152 Martinsried, Germany. einsle@caltech.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-552
A
485Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W)Mutation(s): 0 
Gene Names: nrfA
EC: 1.7.2.2
Find proteins for Q9S1E5 (Wolinella succinogenes (strain ATCC 29543 / DSM 1740 / LMG 7466 / NCTC 11488 / FDC 602W))
Go to UniProtKB:  Q9S1E5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YT3
Query on YT3

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Download CCD File 
A
YTTRIUM (III) ION
Y
GRTBAGCGDOYUBE-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
HOA
Query on HOA

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Download CCD File 
A
HYDROXYAMINE
H3 N O
AVXURJPOCDRRFD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.186 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 119.891α = 90.00
b = 119.891β = 90.00
c = 186.224γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description