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 (software)

Macromolecule Content

• Total Structure Weight: 109.29 kDa 
• Atom Count: 8781 
• Residue Count: 1008 
• Unique protein chains: 1

3H4F

Met62Leu variant of nitrite reductase from Alcaligenes faeclis

• DOI: 10.2210/pdb3H4F/pdb

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


• Deposited: 2009-04-19 Released: 2010-02-02 
• Deposition Author(s): MacPherson, I.S., Rosell, F.I., Scofield, M., Mauk, A.G., Murphy, M.E.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.227 
• R-Value Work: 0.166 
• R-Value Observed: 0.170 

Literature

Directed evolution of copper nitrite reductase to a chromogenic reductant.

Macpherson, I.S., Rosell, F.I., Scofield, M., Mauk, A.G., Murphy, M.E.

(2010) Protein Eng Des Sel 23: 137-145

• PubMed: 20083495 
• DOI: 10.1093/protein/gzp084
• Primary Citation of Related Structures:  
  3H56, 3H4H, 3H4F


• PubMed Abstract: 
  

Directed evolution methods were developed for Cu-containing nitrite reductase (NiR) from Alcaligenes faecalis S-6. The PCR cloning strategy allows for the efficient production of libraries of 100 000 clones by a modification of a megaprimer-based whole-plasmid synthesis reaction. The high-throughput screen includes colony lift onto a nylon membrane and subsequent lysis of NiR-expressing colonies in the presence of Cu(2+) ions for copper incorporation into intracellularly expressed NiR. Addition of a chromogenic substrate, 3, 3'-diaminobenzidine (DAB), results in deposition of red, insoluble color at the site of oxidation by functional NiR. Twenty-thousand random variants of NiR were screened for improved function with DAB as a reductant, and five variants were identified. These variants were shuffled and screened, yielding two double variants. An analog of the DAB substrate, o-dianisidine, which is oxidized to a water-soluble product was used for functional characterization. The double variant M150L/F312C was most proficient at o-dianisidine oxidation with dioxygen as the electron acceptor (5.5X wt), and the M150L single variant was most proficient at o-dianisidine oxidation with nitrite as the electron acceptor (8.5X wt). The library generation and screening method can be employed for evolving new reductase functions in NiR and for screening of efficient folding of engineered NiRs.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Copper-containing nitrite reductase	A, B, C	336	Alcaligenes faecalis	Mutation(s): 1  Gene Names: nir, nirK EC: 1.7.2.1
Find proteins for P38501 (Alcaligenes faecalis) Explore P38501  Go to UniProtKB:  P38501

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	A, B, C	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.227 
• R-Value Work: 0.166 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.132	α = 90
b = 102.223	β = 90
c = 146.145	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-04-19 
• Released Date: 2010-02-02 
Deposition Author(s): MacPherson, I.S., Rosell, F.I., Scofield, M., Mauk, A.G., Murphy, M.E.P.

Revision History 

• Version 1.0: 2010-02-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance