1GQ1

CYTOCHROME CD1 NITRITE REDUCTASE, Y25S mutant, OXIDISED FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Kinetic Properties of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase with the D1 Heme Active Site Ligand Tyrosine 25 Replaced by Serine

Gordon, E.H.J.Sjogren, T.Lofqvist, M.Richter, C.D.Allen, J.Higham, C.Hajdu, J.Fulop, V.Ferguson, S.J.

(2003) J.Biol.Chem. 278: 11773

  • DOI: 10.1074/jbc.M211886200

  • PubMed Abstract: 
  • The 1.4-A crystal structure of the oxidized state of a Y25S variant of cytochrome cd(1) nitrite reductase from Paracoccus pantotrophus is described. It shows that loss of Tyr(25), a ligand via its hydroxy group to the iron of the d(1) heme in the oxi ...

    The 1.4-A crystal structure of the oxidized state of a Y25S variant of cytochrome cd(1) nitrite reductase from Paracoccus pantotrophus is described. It shows that loss of Tyr(25), a ligand via its hydroxy group to the iron of the d(1) heme in the oxidized (as prepared) wild-type enzyme, does not result in a switch at the c heme of the unusual bishistidinyl coordination to the histidine/methionine coordination seen in other conformations of the enzyme. The Ser(25) side chain is seen in two positions in the d(1) heme pocket with relative occupancies of approximately 7:3, but in neither case is the hydroxy group bound to the iron atom; instead, a sulfate ion from the crystallization solution is bound between the Ser(25) side chain and the heme iron. Unlike the wild-type enzyme, the Y25S mutant is active as a reductase toward nitrite, oxygen, and hydroxylamine without a reductive activation step. It is concluded that Tyr(25) is not essential for catalysis of reduction of any substrate, but that the requirement for activation by reduction of the wild-type enzyme is related to a requirement to drive the dissociation of this residue from the active site. The Y25S protein retains the d(1) heme less well than the wild-type protein, suggesting that the tyrosine residue has a role in stabilizing the binding of this cofactor.


    Related Citations: 
    • The Anatomy of a Bifunctional Enzyme: Structural Basis for Reduction of Oxygen to Water and Synthesis of Nitric Oxide by Cytochrome Cd1
      Fulop, V.,Moir, J.W.B.,Ferguson, S.J.,Hajdu, J.
      (1995) Cell 81: 369


    Organizational Affiliation

    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME CD1 NITRITE REDUCTASE
A, B
567Paracoccus pantotrophusGene Names: nirS
EC: 1.7.99.1, 1.7.2.1
Find proteins for P72181 (Paracoccus pantotrophus)
Go to UniProtKB:  P72181
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-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
DHE
Query on DHE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 106.797α = 90.00
b = 60.600β = 112.33
c = 100.340γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-11-28
    Type: Initial release
  • Version 1.1: 2011-10-19
    Type: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2018-01-17
    Type: Data collection