PDBsum entry 1nir

Nitrite reductase

PDB id: 1nir

Contents

Protein chains

538 a.a. *

Ligands

PO4 ×2

_OH ×2

HEC ×2

DHE ×2

Metals

_CL ×2

Waters ×870

* Residue conservation analysis

PDB id:

1nir

Name:

Nitrite reductase

Title:

Oxydized nitrite reductase from pseudomonas aeruginosa

Structure:

Nitrite reductase. Chain: a, b. Other_details: each sub-unit (a, b) linking one phosphate ion and one chloride ion

Source:

Pseudomonas aeruginosa. Organism_taxid: 287. Cellular_location: periplasmic space. Other_details: nctc 6750

Biol. unit:

Homo-Dimer (from PDB file)

Resolution:

2.15Å R-factor: 0.209 R-free: 0.242

Authors:

D.Nurizzo,M.Tegoni,C.Cambillau

Key ref:

D.Nurizzo et al. (1997). N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa. Structure, 5, 1157-1171. PubMed id: 9331415 DOI: 10.1016/S0969-2126(97)00267-0

Date:

17-Jun-97 Release date: 03-Dec-97

Protein chains

P24474  (NIRS_PSEAE) -  Nitrite reductase from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

Seq: 568 a.a.

Struc: 539 a.a.

Enzyme reactions

• Enzyme class 2: 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
• Enzyme class 3: E.C.1.7.99.1 - hydroxylamine reductase.
• Reaction: A + NH4⁺ + H2O = hydroxylamine + AH2 + H⁺
• Cofactor: Flavoprotein

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/S0969-2126(97)00267-0

Structure 5:1157-1171 (1997)

PubMed id: 9331415

N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa.

D.Nurizzo, M.C.Silvestrini, M.Mathieu, F.Cutruzzolà, D.Bourgeois, V.Fülöp, J.Hajdu, M.Brunori, M.Tegoni, C.Cambillau.

ABSTRACT

BACKGROUND: Nitrite reductase from Pseudomonas aeruginosa (NiR-Pa) is a dimer consisting of two identical 60 kDa subunits, each of which contains one c and one d1 heme group. This enzyme, a soluble component of the electron-transfer chain that uses nitrate as a source of energy, can be induced by the addition of nitrate to the bacterial growth medium. NiR-Pa catalyzes the reduction of nitrite (NO2-) to nitric oxide (NO); in vitro, both cytochrome c551 and azurin are efficient electron donors in this reaction. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. RESULTS: The structure of the orthorhombic form (P2(1)2(1)2) of oxidized NiR-Pa was solved at 2.15 A resolution, using molecular replacement with the coordinates of the NiR from Thiosphaera pantotropha (NiR-Tp) as the starting model. Although the d1-heme domains are almost identical in both enzyme structures, the c domain of NiR-Pa is more like the classical class I cytochrome-c fold because it has His51 and Met88 as heme ligands, instead of His17 and His69 present in NiR-Tp. In addition, the methionine-bearing loop, which was displaced by His17 of the NiR-Tp N-terminal segment, is back to normal in our structure. The N-terminal residues (5/6-30) of NiR-Pa and NiR-Tp have little sequence identity. In Nir-Pa, this N-terminal segment of one monomer crosses the dimer interface and wraps itself around the other monomer. Tyr10 of this segment is hydrogen bonded to an hydroxide ion--the sixth ligand of the d1-heme Fe, whereas the equivalent residue in NiR-Tp, Tyr25, is directly bound to the Fe. CONCLUSIONS: Two ligands of hemes c and d1 differ between the two known NiR structures, which accounts for the fact that they have quite different spectroscopic and kinetic features. The unexpected domain-crossing by the N-terminal segment of NiR-Pa is comparable to that of 'domain swapping' or 'arm exchange' previously observed in other systems and may explain the observed cooperativity between monomers of dimeric NiR-Pa. In spite of having similar sequence and fold, the different kinetic behaviour and the spectral features of NiR-Pa and NiR-Tp are tuned by the N-terminal stretch of residues. A further example of this may come from another NiR, from Pseudomonas stutzeri, which has an N terminus very different from that of the two above mentioned NiRs.

Selected figure(s)

Figure 6.
Figure 6. Water-accessible surface area of NiR-Pa monomer A, slabbed at the level of the d[1] heme. Water molecules are colored in blue, the d[1] heme in red and the phosphate ion in green. The channel starting from the d[1] heme and leading to the `back door' is located between the d[1] heme and the phosphate ion.

The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 1157-1171) copyright 1997.

Figure was selected by an automated process.