PDBsum entry 1zds

Oxidoreductase

PDB id: 1zds

Contents

Protein chains

335 a.a. *

Ligands

ACM ×6

Metals

_CU ×6

Waters ×1143

* Residue conservation analysis

PDB id:

1zds

Name:

Oxidoreductase

Title:

Crystal structure of met150gly afnir with acetamide bound

Structure:

Copper-containing nitrite reductase. Chain: a, b, c. Synonym: cu-nir. Engineered: yes. Mutation: yes

Source:

Alcaligenes faecalis. Organism_taxid: 511. Gene: nirk, nir

Biol. unit:

Trimer (from PQS)

Resolution:

1.55Å R-factor: 0.183 R-free: 0.214

Authors:

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

Key ref:

H.J.Wijma et al. (2006). A rearranging ligand enables allosteric control of catalytic activity in copper-containing nitrite reductase. J Mol Biol, 358, 1081-1093. PubMed id: 16574144 DOI: 10.1016/j.jmb.2006.02.042

Date:

14-Apr-05 Release date: 28-Mar-06

Protein chains

P38501  (NIR_ALCFA) -  Copper-containing nitrite reductase from Alcaligenes faecalis

Seq: 376 a.a.

Struc: 335 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.7.2.1 - nitrite reductase (NO-forming).
• Reaction: nitric oxide + Fe(III)-[cytochrome c] + H2O = Fe(II)-[cytochrome c] + nitrite + 2 H⁺
• Cofactor: Cu cation or Fe cation; FAD

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2006.02.042

J Mol Biol 358:1081-1093 (2006)

PubMed id: 16574144

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

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

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.

Selected figure(s)

Figure 4.

Figure 7.
Figure 7. Crystal structures of the type-1 copper sites. Identical views are given for (a), (b) and (c). Foreground: Ala61–Phe64, His95. Background: Cys136, Trp144, His145, and Gly150 (mutant) or Met150 (wt). The type-1 copper is a salmon colored sphere. The σ[A] weighted 2F[o]−F[c] electron density maps are contoured at 1σ. (a) The structure of M150G-DMS. (b) The structure of M150G-acetamide. (c) Stereo stick representation of wt NiR superimposed with M150G-DMS and M150G-acetamide. The carbon atoms are colored white, slate, and green for wt NiR, M150G-DMS, and M150G-acetamide, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 1081-1093) copyright 2006.

Figures were selected by the author.