1HZV

DOMAIN SWING UPON HIS TO ALA MUTATION IN NITRITE REDUCTASE OF PSEUDOMONAS AERUGINOSA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.282 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Domain swing upon His to Ala mutation in nitrite reductase of Pseudomonas aeruginosa.

Brown, K.Roig-Zamboni, V.Cutruzzola, F.Arese, M.Sun, W.Brunori, M.Cambillau, C.Tegoni, M.

(2001) J.Mol.Biol. 312: 541-554

  • DOI: 10.1006/jmbi.2001.4986
  • Primary Citation of Related Structures:  1HZU

  • PubMed Abstract: 
  • The nitrite reductase (NIR) from Pseudomonas aeruginosa (NIR-Pa) is a soluble enzyme catalysing the reduction of nitrite (NO2(-)) to nitric oxide (NO). The enzyme is a 120 kDa homodimer, in which the monomers carry a c-heme domain and a d(1)-heme dom ...

    The nitrite reductase (NIR) from Pseudomonas aeruginosa (NIR-Pa) is a soluble enzyme catalysing the reduction of nitrite (NO2(-)) to nitric oxide (NO). The enzyme is a 120 kDa homodimer, in which the monomers carry a c-heme domain and a d(1)-heme domain. The structures of the enzyme in both the oxidised and reduced state were solved previously and indicate His327 and His369 as putative catalytic residues. The kinetic characterisation of site-directed mutants has shown that the substitution of either one of these two His with Ala dramatically reduces the physiologically relevant reactivity towards nitrite, leaving the reactivity towards oxygen unaffected. The three-dimensional structures of P. aeruginosa NIR mutant H327A, and H369A in complex with NO have been solved by multiple wavelength anomalous dispersion (MAD), using the iron anomalous signal, and molecular replacement techniques. In both refined crystal structures the c-heme domain, whilst preserving its classical c-type cytochrome fold, has undergone a 60 degrees rigid-body rotation around an axis parallel with the pseudo 8-fold axis of the beta-propeller, and passing through residue Gln115. Even though the distance between the Fe ions of the c and d(1)-heme remains 21 A, the edge-to-edge distance between the two hemes has increased by 5 A. Furthermore the distal side of the d(1)-heme pocket appears to have undergone structural re-arrangement and Tyr10 has moved out of the active site. In the H369A-NO complex, the position and orientation of NO is significantly different from that of the NO bound to the reduced wild-type structure. Our results provide insight into the flexibility of the enzyme and the distinction between nitrite and oxidase reduction mechanisms. Moreover they demonstrate that the two histidine residues play a crucial role in the physiological activity of nitrite reduction, ligand binding and in the structural organisation of nitrite reductase from P. aeruginosa.


    Related Citations: 
    • The Nitrite Reductase from Pseudomonas aeruginosa: Essential Role of Two Active-site Histidines in the Catalytic and Structural Properties.
      Cutruzzola, F.,Brown, K.,Wilson, E.K.,Bellelli, A.,Arese, M.,Tegoni, M.,Cambillau, C.,Brunori, M.
      (2001) Proc.Natl.Acad.Sci.USA 98: 2232


    Organizational Affiliation

    Architecture et Fonction des Macromolécules Biologiques U.M.R.6098, C.N.R.S and Universités d'Aix-Marseille I and II, 31, Ch.Joseph Aiguier, Marseille Cedex 20, F-13402, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRITE REDUCTASE
A
543Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)Gene Names: nirS
EC: 1.7.99.1, 1.7.2.1
Find proteins for P24474 (Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228))
Go to UniProtKB:  P24474
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download SDF File 
Download CCD File 
A
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
NO
Query on NO

Download SDF File 
Download CCD File 
A
NITRIC OXIDE
Nitrogen monoxide
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
DHE
Query on DHE

Download SDF File 
Download CCD File 
A
HEME D
C34 H32 Fe N4 O10
XLQCGNUTSJTZNF-SOFPVUHFDM
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.83 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.282 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.744α = 90.00
b = 94.744β = 90.00
c = 159.901γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MLPHAREphasing
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Database references