1KCB

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitrite ReductaseA340Achromobacter cycloclastesMutation(s): 1 
Gene Names: nirK
EC: 1.7.99.3 (PDB Primary Data), 1.7.2.1 (UniProt)
Find proteins for P25006 (Achromobacter cycloclastes)
Explore P25006 
Go to UniProtKB:  P25006
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download CCD File 
A
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
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 = 98.16α = 90
b = 98.16β = 90
c = 98.16γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

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