4CSP

Structure of the F306C mutant of nitrite reductase from Achromobacter xylosoxidans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Impact of Residues Remote from the Catalytic Centre on Enzyme Catalysis of Copper Nitrite Reductase.

Leferink, N.G.H.Antonyuk, S.V.Houwman, J.A.Scrutton, N.S.Eady, R.R.Hasnain, S.S.

(2014) Nat Commun 5: 4395

  • DOI: https://doi.org/10.1038/ncomms5395
  • Primary Citation of Related Structures:  
    4CSP, 4CSZ

  • PubMed Abstract: 

    Enzyme mechanisms are often probed by structure-informed point mutations and measurement of their effects on enzymatic properties to test mechanistic hypotheses. In many cases, the challenge is to report on complex, often inter-linked elements of catalysis. Evidence for long-range effects on enzyme mechanism resulting from mutations remains sparse, limiting the design/redesign of synthetic catalysts in a predictable way. Here we show that improving the accessibility of the active site pocket of copper nitrite reductase by mutation of a surface-exposed phenylalanine residue (Phe306), located 12 Å away from the catalytic site type-2 Cu (T2Cu), profoundly affects intra-molecular electron transfer, substrate-binding and catalytic activity. Structures and kinetic studies provide an explanation for the lower affinity for the substrate and the alteration of the rate-limiting step in the reaction. Our results demonstrate that distant residues remote from the active site can have marked effects on enzyme catalysis, by driving mechanistic change through relatively minor structural perturbations.


  • Organizational Affiliation

    1] Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK [2].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASEA,
B [auth F]
335Achromobacter xylosoxidansMutation(s): 1 
EC: 1.7.2.1
UniProt
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans)
Explore O68601 
Go to UniProtKB:  O68601
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68601
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
G [auth A],
M [auth F]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
H [auth A]
K [auth F]
L [auth F]
E [auth A],
F [auth A],
H [auth A],
K [auth F],
L [auth F],
N [auth F],
O [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth F],
J [auth F]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.99α = 90
b = 89.99β = 90
c = 289.45γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Derived calculations
  • Version 1.2: 2017-09-13
    Changes: Data collection, Structure summary
  • Version 1.3: 2023-12-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description