2XX1

STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS complexed with nitrite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase.

Leferink, N.G.H.Han, C.Antonyuk, S.V.Heyes, D.J.Rigby, S.E.J.Hough, M.A.Eady, R.R.Scrutton, N.S.Hasnain, S.S.

(2011) Biochemistry 50: 4121

  • DOI: https://doi.org/10.1021/bi200246f
  • Primary Citation of Related Structures:  
    2XWZ, 2XX0, 2XX1, 2XXF

  • PubMed Abstract: 

    We demonstrated recently that two protons are involved in reduction of nitrite to nitric oxide through a proton-coupled electron transfer (ET) reaction catalyzed by the blue Cu-dependent nitrite reductase (Cu NiR) of Alcaligenes xylosoxidans (AxNiR). Here, the functionality of two putative proton channels, one involving Asn90 and the other His254, is studied using single (N90S, H254F) and double (N90S--H254F) mutants. All mutants studied are active, indicating that protons are still able to reach the active site. The H254F mutation has no effect on the catalytic activity, while the N90S mutation results in ~70% decrease in activity. Laser flash-photolysis experiments show that in H254F and wild-type enzyme electrons enter at the level of the T1Cu and then redistribute between the two Cu sites. Complete ET from T1Cu to T2Cu occurs only when nitrite binds at the T2Cu site. This indicates that substrate binding to T2Cu promotes ET from T1Cu, suggesting that the enzyme operates an ordered mechanism. In fact, in the N90S and N90S--H254F variants, where the T1Cu site redox potential is elevated by ∼60 mV, inter-Cu ET is only observed in the presence of nitrite. From these results it is evident that the Asn90 channel is the main proton channel in AxNiR, though protons can still reach the active site if this channel is disrupted. Crystallographic structures provide a clear structural rationale for these observations, including restoration of the proton delivery via a significant movement of the loop connecting the T1Cu ligands Cys130 and His139 that occurs on binding of nitrite. Notably, a role for this loop in facilitating interaction of cytochrome c(551) with Cu NiR has been suggested previously based on a crystal structure of the binary complex.


  • Organizational Affiliation

    Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
A, B, C, D, E
A, B, C, D, E, F
336Achromobacter 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
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
IA [auth E]
J [auth A]
JA [auth E]
CA [auth D],
DA [auth D],
IA [auth E],
J [auth A],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
MA [auth E],
Q [auth B],
R [auth B],
RA [auth F],
S [auth B],
SA [auth F],
T [auth B],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CU
Query on CU

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
FA [auth E]
G [auth A]
GA [auth E]
AA [auth D],
BA [auth D],
FA [auth E],
G [auth A],
GA [auth E],
H [auth A],
N [auth B],
O [auth B],
OA [auth F],
PA [auth F],
U [auth C],
V [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
NO2
Query on NO2

Download Ideal Coordinates CCD File 
EA [auth E]
HA [auth E]
I [auth A]
NA [auth F]
P [auth B]
EA [auth E],
HA [auth E],
I [auth A],
NA [auth F],
P [auth B],
QA [auth F]
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.67α = 90
b = 174.65β = 90
c = 180.65γ = 90
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: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description