Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 111.86 kDa 
• Atom Count: 8790 
• Residue Count: 1009 
• Unique protein chains: 1

2PPF

Reduced mutant D98N of AfNiR exposed to nitric oxide

• DOI: 10.2210/pdb2PPF/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Alcaligenes faecalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-04-28 Released: 2008-01-15 
• Deposition Author(s): Tocheva, E.I., Murphy, M.E.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.170 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Literature

Stable copper-nitrosyl formation by nitrite reductase in either oxidation state

Tocheva, E.I., Rosell, F.I., Mauk, A.G., Murphy, M.E.

(2007) Biochemistry 46: 12366-12374

• PubMed: 17924665 
• DOI: 10.1021/bi701205j
• Primary Citation of Related Structures:  
  2PPF, 2PPE, 2PPD, 2PPC


• PubMed Abstract: 
  

Nitrite reductase (NiR) is an enzyme that uses type 1 and type 2 copper sites to reduce nitrite to nitric oxide during bacterial denitrification. A copper-nitrosyl intermediate is a proposed, yet poorly characterized feature of the NiR catalytic cycle. This intermediate is formally described as Cu(I)-NO+ and is proposed to be formed at the type 2 copper site after nitrite binding and electron transfer from the type 1 copper site. In this study, copper-nitrosyl complexes were formed by prolonged exposure of exogenous NO to crystals of wild-type and two variant forms of NiR from Alcaligenes faecalis (AfNiR), and the structures were determined to 1.8 A or better resolution. Exposing oxidized wild-type crystals to NO results in the reverse reaction and formation of nitrite that remains bound at the active site. In a type 1 copper site mutant (H145A) that is incapable of electron transfer to the type 2 site, the reverse reaction is not observed. Instead, in both oxidized and reduced H145A crystals, NO is observed bound in a side-on manner to the type 2 copper. In AfNiR, Asp98 forms hydrogen bonds to both substrate and product bound to the type 2 Cu. In the D98N variant, NO is bound side-on but is more disordered when observed for the wild-type enzyme. The solution EPR spectra of the crystallographically characterized NiR-NO complexes indicate the presence of an oxidized type 2 copper site and thus are interpreted as resulting from stable copper-nitrosyls and formally assigned as Cu(II)-NO-. A reaction scheme in which a second NO molecule is oxidized to nitrite can account for the formation of a Cu(II)-NO- species after exposure of the oxidized H145A variant to NO gas.

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Organizational Affiliation: 

Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver BC, V6T 1Z3, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A, B, C	341	Alcaligenes faecalis	Mutation(s): 1  Gene Names: nirK, nir EC: 1.7.2.1
Find proteins for P38501 (Alcaligenes faecalis) Explore P38501  Go to UniProtKB:  P38501

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CU1	A, B, C	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N
CU	A, B, C	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
ACT	A, B, C	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NO	A, B, C	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYAM

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.170 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.423	α = 90
b = 102.422	β = 90
c = 146.123	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-04-28 
• Released Date: 2008-01-15 
Deposition Author(s): Tocheva, E.I., Murphy, M.E.P.

Revision History 

• Version 1.0: 2008-01-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance