1ZDS

Crystal Structure of Met150Gly AfNiR with Acetamide Bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A rearranging ligand enables allosteric control of catalytic activity in copper-containing nitrite reductase.

Wijma, H.J.Macpherson, I.Alexandre, M.Diederix, R.E.Canters, G.W.Murphy, M.E.Verbeet, M.P.

(2006) J Mol Biol 358: 1081-1093

  • DOI: https://doi.org/10.1016/j.jmb.2006.02.042
  • Primary Citation of Related Structures:  
    1ZDQ, 1ZDS

  • PubMed Abstract: 

    In Cu-containing nitrite reductase from Alcaligenes faecalis S-6 the axial methionine ligand of the type-1 site was replaced (M150G) to make the copper ion accessible to external ligands that might affect the enzyme's catalytic activity. The type-1 site optical spectrum of M150G (A(460)/A(600)=0.71) differs significantly from that of the native nitrite reductase (A(460)/A(600)=1.3). The midpoint potential of the type-1 site of nitrite reductase M150G (E(M)=312(+/-5)mV versus hydrogen) is higher than that of the native enzyme (E(M)=213(+/-5)mV). M150G has a lower catalytic activity (k(cat)=133(+/-6)s(-1)) than the wild-type nitrite reductase (k(cat)=416(+/-10)s(-1)). The binding of external ligands to M150G restores spectral properties, midpoint potential (E(M)<225mV), and catalytic activity (k(cat)=374(+/-28)s(-1)). Also the M150H (A(460)/A(600)=7.7, E(M)=104(+/-5)mV, k(cat)=0.099(+/-0.006)s(-1)) and M150T (A(460)/A(600)=0.085, E(M)=340(+/-5)mV, k(cat)=126(+/-2)s(-1)) variants were characterized. Crystal structures show that the ligands act as allosteric effectors by displacing Met62, which moves to bind to the Cu in the position emptied by the M150G mutation. The reconstituted type-1 site has an otherwise unaltered geometry. The observation that removal of an endogenous ligand can introduce allosteric control in a redox enzyme suggests potential for structural and functional flexibility of copper-containing redox sites.


  • Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Copper-containing nitrite reductase
A, B, C
336Alcaligenes faecalisMutation(s): 1 
Gene Names: nirKnir
EC: 1.7.2.1
UniProt
Find proteins for P38501 (Alcaligenes faecalis)
Explore P38501 
Go to UniProtKB:  P38501
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38501
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
H [auth B]
I [auth B]
L [auth C]
D [auth A],
E [auth A],
H [auth B],
I [auth B],
L [auth C],
M [auth C]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
ACM
Query on ACM

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
J [auth B]
K [auth B]
N [auth C]
F [auth A],
G [auth A],
J [auth B],
K [auth B],
N [auth C],
O [auth C]
ACETAMIDE
C2 H5 N O
DLFVBJFMPXGRIB-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ACM Binding MOAD:  1ZDS Kd: 7.13e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.645α = 90
b = 102.365β = 90
c = 146.189γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection