Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 127.95 kDa 
• Atom Count: 9938 
• Modelled Residue Count: 1110 
• Deposited Residue Count: 1134 
• Unique protein chains: 1

1AOQ

CYTOCHROME CD1 NITRITE REDUCTASE WITH SUBSTRATE AND PRODUCT BOUND

• PDB DOI: 10.2210/pdb1AOQ/pdb

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


• Deposited: 1997-07-09 Released: 1998-02-04 
• Deposition Author(s): Williams, P.A., Fulop, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.197 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 

Literature

Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme.

Williams, P.A., Fulop, V., Garman, E.F., Saunders, N.F., Ferguson, S.J., Hajdu, J.

(1997) Nature 389: 406-412

• PubMed: 9311786 
• DOI: 10.1038/38775
• Primary Citation of Related Structures:  
  1AOF, 1AOM, 1AOQ


• PubMed Abstract: 
  

Cytochrome cd1 nitrite reductase catalyses the conversion of nitrite to nitric oxide in the nitrogen cycle. The crystal structure of the oxidized enzyme shows that the d1 haem iron of the active site is ligated by His/Tyr side chains, and the c haem iron is ligated by a His/His ligand pair. Here we show that both haems undergo re-ligation during catalysis. Upon reduction, the tyrosine ligand of the d1 haem is released to allow substrate binding. Concomitantly, a refolding of the cytochrome c domain takes place, resulting in an unexpected change of the c haem iron coordination from His 17/His 69 to Met106/His69. This step is similar to the last steps in the folding of cytochrome c. The changes must affect the redox potential of the haems, and suggest a mechanism by which internal electron transfer is regulated. Structures of reaction intermediates show how nitric oxide is formed and expelled from the active-site iron, as well as how both haems return to their starting coordination. These results show how redox energy can be switched into conformational energy within a haem protein.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, University of Oxford, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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], G [auth B]	HEME D C34 H32 Fe N4 O10 XLQCGNUTSJTZNF-SOFPVUHFDM
HEM	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
2NO	E [auth A]	NITROGEN DIOXIDE N O2 IOVCWXUNBOPUCH-QEZKKOIZCP
NO	H [auth B]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYAM

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.197 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.7	α = 90
b = 60.6	β = 112.3
c = 100.1	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-07-09 
• Released Date: 1998-02-04 
Deposition Author(s): Williams, P.A., Fulop, V.

Revision History  

• Version 1.0: 1998-02-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance