1QKS

CYTOCHROME CD1 NITRITE REDUCTASE, OXIDISED FORM

• PDB DOI:  https://doi.org/10.2210/pdb1QKS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Paracoccus pantotrophus
• Mutation(s): No 


• Deposited: 1999-08-05 Released: 1999-08-18 
• Deposition Author(s): Fulop, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.200 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 

Literature

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., Ferguson, S.J., Hajdu, J.

(1995) Cell 81: 369-377

• PubMed: 7736589 
• DOI: https://doi.org/10.1016/0092-8674(95)90390-9
• Primary Citation of Related Structures:  
  1QKS


• PubMed Abstract: 
  

Cytochrome cd1-nitrite reductase is a bifunctional enzyme that catalyzes the one-electron reduction of nitrite to nitric oxide and the four-electron reduction of oxygen to water. The 1.55 A crystal structure of the dimeric enzyme from Thiosphaera pantotropha is reported here. The protein was sequenced from the X-ray structure. Each subunit contains a covalent c heme with two axial His ligands (His-17, His-69) and a unique noncovalent d1 heme ligated by Tyr-25 and His-200. The d1 heme is the mononuclear iron center where both oxygen and nitrite reduction take place. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis.

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Related Citations: 

• Cytochrome Cd1 Structure: Unusual Haem Environments in a Nitrite Reductase and Analysis of Factors Contributing to Beta-Propeller Folds
  Baker, S.C., Saunders, N.F.W., Willis, A.C., Ferguson, S.J., Hajdu, J., Fulop, V.
  (1997) J Mol Biol 269: 440

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, University of Oxford, England.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 129.09 kDa 
• Atom Count: 10,463 
• Modelled Residue Count: 1,118 
• Deposited Residue Count: 1,134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME CD1 NITRITE REDUCTASE	A, B	567	Paracoccus pantotrophus	Mutation(s): 0  Gene Names: nirS EC: 1.7.2.1 (UniProt), 1.7.99.1 (UniProt)
UniProt
Find proteins for P72181 (Paracoccus pantotrophus) Explore P72181  Go to UniProtKB:  P72181

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DHE	D [auth A], L [auth B]	HEME D C34 H32 Fe N4 O10 XLQCGNUTSJTZNF-SOFPVUHFDM
HEC	C [auth A], K [auth B]	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
SO4	I [auth A], J [auth A], P [auth B], Q [auth B], R [auth B], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.200 
• R-Value Work: 0.185 
• R-Value Observed: 0.185 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.4	α = 90
b = 60.6	β = 112.3
c = 100.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-08-18 
Deposition Author(s): Fulop, V.

Revision History  

• Version 1.0: 1999-08-18
  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: 2019-01-16
  Changes: Data collection, Database references
• Version 1.4: 2019-10-09
  Changes: Data collection, Database references, Derived calculations