1GJQ

Pseudomonas aeruginosa cd1 nitrite reductase reduced cyanide complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Cyanide Binding to Cd(1) Nitrite Reductase from Pseudomonas Aeruginosa: Role of the Active-Site His369 in Ligand Stabilization.

Sun, W., Arese, M., Brunori, M., Nurizzo, D., Brown, K., Cambillau, C., Tegoni, M., Cutruzzola, F.

(2002) Biochem Biophys Res Commun 291: 1

  • DOI: 10.1006/bbrc.2002.6391
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Cyanide binding to fully reduced Pseudomonas aeruginosa cd(1) nitrite reductase (Pa cd(1) NiR) has been investigated for the wild-type enzyme and a site-directed mutant in which the active-site His369 was replaced by Ala. This mutation reduces the af ...

    Cyanide binding to fully reduced Pseudomonas aeruginosa cd(1) nitrite reductase (Pa cd(1) NiR) has been investigated for the wild-type enzyme and a site-directed mutant in which the active-site His369 was replaced by Ala. This mutation reduces the affinity toward cyanide (by approximately 13-fold) and especially decreases the rate of binding of cyanide to the reduced d(1) heme (by approximately 100-fold). The crystal structure of wild-type reduced Pa cd(1) NiR saturated with cyanide was determined to a resolution of 2.7 A. Cyanide binds to the iron of the d(1) heme, with an Fe-C-N angle of 168 degrees for both subunits of the dimer and only His369 is within hydrogen bonding distance of the nitrogen atom of the ligand. These results suggest that in Pa cd(1) NiR the invariant distal residue His369 plays a dominant role in controlling the binding of anionic ligands and allow the discussion of the mechanism of cyanide binding to the wild-type enzyme.

    Organizational Affiliation: 

    Dipartimento di Scienze Biochimiche A. Rossi Fanelli and Centro di Biologia Molecolare del CNR, Università di Roma La Sapienza, Rome, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRITE REDUCTASEA, B543Pseudomonas aeruginosaMutation(s): 0 
EC: 1.9.3.2 (PDB Primary Data), 1.7.2.1 (UniProt), 1.7.99.1 (UniProt)
Find proteins for P24474 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P24474 
Go to UniProtKB:  P24474
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHE
Query on DHE
Download CCD File 
A, B
HEME D
C34 H32 Fe N4 O10
XLQCGNUTSJTZNF-SOFPVUHFDM		 Ligand Interaction
HEC
Query on HEC
Download CCD File 
A, B
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N		 Ligand Interaction
CYN
Query on CYN
Download CCD File 
A, B
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.4α = 90
b = 88.6β = 90
c = 113.4γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations