Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 37.20 kDa 
• Atom Count: 2745 
• Modelled Residue Count: 333 
• Deposited Residue Count: 340 
• Unique protein chains: 1

1KCB

Crystal Structure of a NO-forming Nitrite Reductase Mutant: an Analog of a Transition State in Enzymatic Reaction

• PDB DOI: 10.2210/pdb1KCB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Achromobacter cycloclastes
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-11-07 Released: 2003-11-04 
• Deposition Author(s): Liu, S.Q., Chang, T., Liu, M.Y., LeGall, J., Chang, W.C., Zhang, J.P., Liang, D.C., Chang, W.R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.204 
• R-Value Work: 0.170 

Literature

Crystal structure of a NO-forming nitrite reductase mutant: an analog of a transition state in enzymatic reaction

Liu, S.Q., Chang, T., Liu, M.Y., LeGall, J., Chang, W.C., Zhang, J.P., Liang, D.C., Chang, W.R.

(2003) Biochem Biophys Res Commun 302: 568-574

• PubMed: 12615072 
• DOI: 10.1016/s0006-291x(03)00166-9
• Primary Citation of Related Structures:  
  1KCB


• PubMed Abstract: 
  

I257E was obtained by site directed mutagenesis of nitrite reductase from Achromobacter cycloclastes. The mutant has no enzyme activity. Its crystal structure determined at 1.65A resolution shows that the side-chain carboxyl group of the mutated residue, Glu257, coordinates with the type 2 copper in the mutant and blocks the contact between the type 2 copper and its solvent channel, indicating that the accessibility of the type 2 copper is essential for maintaining the activity of nitrite reductase. The carboxylate is an analog of the substrate, nitrite, but the distances between the type 2 copper and the two oxygen atoms of the side-chain carboxyl group are reversed in comparison to the binding of nitrite to the native enzyme. In the mutant, both the type 2 copper and the N epsilon atom on the imidazole ring of its coordinated residue His135 move in the substrate binding direction relative to the native enzyme. In addition, an EPR study showed that the type 2 copper in the mutant is in a reduced state. We propose that mutant I257E is in a state corresponding to a transition state in the enzymatic reaction.

---

Organizational Affiliation: 

National laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrite Reductase	A	340	Achromobacter cycloclastes	Mutation(s): 1  Gene Names: nirK EC: 1.7.99.3 (PDB Primary Data), 1.7.2.1 (UniProt)
UniProt
Find proteins for P25006 (Achromobacter cycloclastes) Explore P25006  Go to UniProtKB:  P25006

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.204 
• R-Value Work: 0.170 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.16	α = 90
b = 98.16	β = 90
c = 98.16	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-11-07 
• Released Date: 2003-11-04 
Deposition Author(s): Liu, S.Q., Chang, T., Liu, M.Y., LeGall, J., Chang, W.C., Zhang, J.P., Liang, D.C., Chang, W.R.

Revision History  

• Version 1.0: 2003-11-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations