PDBsum entry 1haw

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Oxidoreductase PDB id
Protein chain
336 a.a. *
Waters ×149
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: X-ray structure of a blue copper nitrite reductase at high ph and in copper free form at 1.9a resolution
Structure: Dissimilatory copper-containing nitrite reductase chain: a. Synonym: nir. Ec:,
Source: Alcaligenes xylosoxydans. Organism_taxid: 85698. Strain: xylosoxidans. Cellular_location: periplasm
Biol. unit: Trimer (from PDB file)
1.90Å     R-factor:   0.172     R-free:   0.199
Authors: M.J.Ellis,F.E.Dodd,R.W.Strange,M.Prudencio,R.R.Sawerseady, S.S.Hasnain
Key ref:
M.J.Ellis et al. (2001). X-ray structure of a blue copper nitrite reductase at high pH and in copper-free form at 1.9 A resolution. Acta Crystallogr D Biol Crystallogr, 57, 1110-1118. PubMed id: 11468394 DOI: 10.1107/S0907444901008654
09-Apr-01     Release date:   02-Aug-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O68601  (O68601_ALCXX) -  Dissimilatory copper-containing nitrite reductase
360 a.a.
336 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nitrogen compound metabolic process   2 terms 
  Biochemical function     oxidoreductase activity     4 terms  


DOI no: 10.1107/S0907444901008654 Acta Crystallogr D Biol Crystallogr 57:1110-1118 (2001)
PubMed id: 11468394  
X-ray structure of a blue copper nitrite reductase at high pH and in copper-free form at 1.9 A resolution.
M.J.Ellis, F.E.Dodd, R.W.Strange, M.Prudêncio, G.Sawers, R.R.Eady, S.S.Hasnain.
Copper-containing nitrite reductases possess a trimeric structure where the catalytic Cu site, located at the monomer-monomer interface, resembles the catalytic sites of a number of Zn enzymes. Nitrite reductase from Alcaligenes xylosoxidans has optimum activity at pH 5.2 which decreases to a negligible level at pH 8. The structure of this nitrite reductase has previously been determined at pH 4.6. It has now been crystallized under new conditions at pH 8.5. Its crystallographic structure provides a structural explanation for the greatly reduced activity of the enzyme at high pH. Characterization of overexpressed protein in solution by EXAFS suggested that the protein lacked Cu in the catalytic type 2 Cu site and that the site was most probably occupied by Zn. Using the anomalous signals from Cu and Zn, the crystal structure revealed that the expressed protein was devoid of Cu in the catalytic site and that only a trace amount (<10%) of Zn was present at this site in the crystal. Despite the close structural similarity of the catalytic site to a number of Zn enzymes, these data suggest that Zn, if it binds at the catalytic copper site, binds weakly in nitrite reductase.
  Selected figure(s)  
Figure 2.
Figure 2 The type 1 Cu site (blue) and the surface hydrophobic residues (green) of (a) ntNiR and (b) rcNiR. The surface above the type 1 Cu site in ntNiR is in a closed conformation. The disordered Met135 (dual conformations shown in red and green) and Met87 cover the type 1 Cu site. In rcNiR, Met135 and Met87 both adopt single conformations which lead to an opening of the surface and the binding of a water (W6) to His139 N 2. A water found in this position in the cupredoxin azurin is associated with electron transfer into the type 1 Cu site (Baker, 1988[Baker, E. N. (1988). J. Mol. Biol. 203, 1071-1075.]; Dodd et al., 1995[Dodd, F. E., Hasnain, S. S., Abraham, Z. H. L., Eady, R. R. & Smith, B. E. (1995). Acta Cryst. D51, 1052-1064.]).
Figure 5.
Figure 5 A comparison is made of the Cu K absorption edge of rcNiR with a reference spectra of the oxidized and reduced type 1 Cu site of ntNiR. The absence of the enhanced `white-line' feature at the rcNiR absorption edge shows that the Cu is reduced.
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 1110-1118) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19586913 S.Brenner, D.J.Heyes, S.Hay, M.A.Hough, R.R.Eady, S.S.Hasnain, and N.S.Scrutton (2009).
Demonstration of proton-coupled electron transfer in the copper-containing nitrite reductases.
  J Biol Chem, 284, 25973-25983.  
18766386 Y.El Khoury, and P.Hellwig (2009).
Infrared spectroscopic characterization of copper-polyhistidine from 1,800 to 50 cm(-1): model systems for copper coordination.
  J Biol Inorg Chem, 14, 23-34.  
18303118 S.Kuznetsova, G.Zauner, T.J.Aartsma, H.Engelkamp, N.Hatzakis, A.E.Rowan, R.J.Nolte, P.C.Christianen, and G.W.Canters (2008).
The enzyme mechanism of nitrite reductase studied at single-molecule level.
  Proc Natl Acad Sci U S A, 105, 3250-3255.  
17148448 F.Jacobson, A.Pistorius, D.Farkas, W.De Grip, O.Hansson, L.Sjölin, and R.Neutze (2007).
pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase.
  J Biol Chem, 282, 6347-6355.
PDB codes: 2dws 2dwt 2dy2
16613859 H.J.Wijma, L.J.Jeuken, M.P.Verbeet, F.A.Armstrong, and G.W.Canters (2006).
A random-sequential mechanism for nitrite binding and active site reduction in copper-containing nitrite reductase.
  J Biol Chem, 281, 16340-16346.  
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