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 PQS (software)

Macromolecule Content

• Total Structure Weight: 37.16 kDa 
• Atom Count: 2892 
• Residue Count: 334 
• Unique protein chains: 1

1WA2

Crystal Structure Of H313Q Mutant Of Alcaligenes Xylosoxidans Nitrite Reductase with nitrite bound

• DOI: 10.2210/pdb1WA2/pdb

• Classification: REDUCTASE
• Organism(s): Achromobacter xylosoxidans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-10-22 Released: 2005-01-04 
• Deposition Author(s): Barrett, M.L., Harris, R.L., Antonyuk, S.V., Strange, R.W., Hough, M.A., Eady, R.R., Sawers, G., Hasnain, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Insights Into Redox Partner Interactions and Substrate Binding in Nitrite Reductase from Alcaligenes Xylosoxidans: Crystal Structures of the Trp138His and His313Gln Mutants

Barrett, M.L., Harris, R.L., Antonyuk, S.V., Hough, M.A., Ellis, M.J., Sawers, G., Eady, R.R., Hasnain, S.S.

(2004) Biochemistry 43: 16311

• PubMed: 15610025 
• DOI: 10.1021/bi048682g
• Primary Citation of Related Structures:  
  1WA2, 1WA1, 1WA0


• PubMed Abstract: 
  

Dissimilatory nitrite reductase catalyses the reduction of nitrite to nitric oxide within the key biological process of denitrification. We present biochemical and structural results on two key mutants, one postulated to be important for the interaction with the partner protein and the other for substrate entry. Trp138, adjacent to one of the type-1 Cu ligands, is one of the residues surrounding a small depression speculated to be important in complex formation with the physiological redox partners, azurin I and II. Our data reveal that the Trp138His mutant is fully active using methyl viologen as an artificial electron donor, but there is a large decrease in activity using azurin I. These observations together with its crystal structure at a high resolution of 1.6 A confirm the importance of Trp138 in electron transfer and thus in productive interaction with azurin. A "hydrophobic pocket" on the protein surface has been identified as the channel through which nitrite may be guided to the catalytic type-2 Cu site. Glu133 and His313 at the opening of the pocket are conserved among most blue and green copper nitrite reductases (CuNiRs). The failure to soak the substrate into our high-resolution crystal form of native and mutant CuNiRs has been linked to the observation of an extraneous poly(ethylene glycol) (PEG) molecule interacting with His313. We present the crystal structure of His313Gln and the substrate-bound mutant at high resolutions of 1.65 and 1.72 A, respectively. The observation of the substrate-bound structure for the His313Gln mutant and inhibitory studies with PEG establishes the role of the hydrophobic pocket as the port of substrate entry.

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Organizational Affiliation: 

Faculty of Applied Sciences, De Montfort University, The Gateway, Leicester, LE1 9BH, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE,	X	336	Achromobacter xylosoxidans	Mutation(s): 1  Gene Names: nir, nirK, ERS451415_02178 EC: 1.7.2.1
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans) Explore O68601  Go to UniProtKB:  O68601

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	X	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	X	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	X	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	X	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
NO2	X	NITRITE ION N O2 IOVCWXUNBOPUCH-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.210 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.641	α = 90
b = 89.641	β = 90
c = 143.569	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-22 
• Released Date: 2005-01-04 
Deposition Author(s): Barrett, M.L., Harris, R.L., Antonyuk, S.V., Strange, R.W., Hough, M.A., Eady, R.R., Sawers, G., Hasnain, S.S.

Revision History 

• Version 1.0: 2005-01-04
  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: 2019-05-22
  Changes: Data collection, Experimental preparation, Other