Time-resolved Infrared Spectroscopy Reveals a Stable Ferric Heme-NO Intermediate in the Reaction of Paracoccus pantotrophus Cytochrome cd 1 Nitrite Reductase with Nitrite

George, Simon J.; Allen, James W. A.; Ferguson, Stuart J.; Thorneley, R. N. F.

doi:10.1074/jbc.m005033200

Cited by 67 publications

(93 citation statements)

References 36 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Nitrite or nitric oxide was bound to the d 1 heme, and His/His coordination of the c heme was observed. In contrast, rapid reaction solution studies, reacting reduced wild type cytochrome cd 1 with nitrite, showed no evidence of His/His coordination of the c heme but only His/Met coordination (24). It is possible, in light of the results presented here, that the same switching of ligands occurred in the nitrite-soaked crystals as proposed here for the Y25S cytochrome cd 1 crystals.…”

Section: Visible Absorption Spectroscopy-contrasting

confidence: 50%

Y25S Variant of Paracoccus pantotrophus Cytochrome cd1 Provides Insight into Anion Binding by d1 Heme and a Rare Example of a Critical Difference between Solution and Crystal Structures

Zajicek

Cheesman

Gordon

et al. 2005

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Tyr25 is a ligand to the active site d 1 heme in as isolated, oxidized cytochrome cd 1 nitrite reductase from Paracoccus pantotrophus. This form of the enzyme requires reductive activation, a process that involves not only displacement of Tyr 25 from the d 1 heme but also switching of the ligands at the c heme from bis-histidinyl to His/Met. A Y25S variant retains this bis-histidinyl coordination in the crystal of the oxidized state that has sulfate bound to the d 1 heme iron. This Y25S form of the enzyme does not require reductive activation, an observation previously interpreted as meaning that the presence of the phenolate oxygen of Tyr 25 is the critical determinant of the requirement for activation. This interpretation now needs re-evaluation because, unexpectedly, the oxidized as prepared Y25S protein, unlike the wild type, has different heme iron ligands in solution at room temperature, as judged by magnetic circular dichroism and electron spin resonance spectroscopies, than in the crystal. In addition, the binding of nitrite and cyanide to oxidized Y25S cytochrome cd 1 is markedly different from the wild type enzyme, thus providing insight into the affinity of the oxidized d 1 heme ring for anions in the absence of the steric barrier presented by Tyr 25 .

show abstract

Section: Visible Absorption Spectroscopy-contrasting

confidence: 50%

Y25S Variant of Paracoccus pantotrophus Cytochrome cd1 Provides Insight into Anion Binding by d1 Heme and a Rare Example of a Critical Difference between Solution and Crystal Structures

Zajicek

Cheesman

Gordon

et al. 2005

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…2 A and B) is thus representative of two processes, namely evolution of the initial mixture to the steady state and formation of the dead-end species. An overall scheme showing the various possible intermediates, as well as information obtained by George et al (20), is depicted in Fig. 3 and detailed in the figure legend.…”

Section: Resultsmentioning

confidence: 99%

The nitrite reductase from Pseudomonas aeruginosa : Essential role of two active-site histidines in the catalytic and structural properties

Cutruzzolà

Brown

Wilson

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

125

View full text Add to dashboard Cite

Cd1 nitrite reductase catalyzes the conversion of nitrite to NO in denitrifying bacteria. Reduction of the substrate occurs at the d1-heme site, which faces on the distal side some residues thought to be essential for substrate binding and catalysis. We report the results obtained by mutating to Ala the two invariant active site histidines, His-327 and His-369, of the enzyme from Pseudomonas aeruginosa. Both mutants have lost nitrite reductase activity but maintain the ability to reduce O 2 to water. Nitrite reductase activity is impaired because of the accumulation of a catalytically inactive form, possibly because the productive displacement of NO from the ferric d 1-heme iron is impaired. Moreover, the two distal His play different roles in catalysis; His-369 is absolutely essential for the stability of the Michaelis complex. The structures of both mutants show (i) the new side chain in the active site, (ii) a loss of density of Tyr-10, which slipped away with the N-terminal arm, and (iii) a large topological change in the whole c-heme domain, which is displaced 20 Å from the position occupied in the wild-type enzyme. We conclude that the two invariant His play a crucial role in the activity and the structural organization of cd 1 nitrite reductase from P. aeruginosa.

show abstract

“…Simple pre-reduction of the enzyme has also resulted in much higher k cat values than could be obtained with the oxidized (as prepared) enzyme for any of the electron donor proteins: cytochrome c 550 , pseudoazurin, or horse heart cytochrome c, in combination with any of the three known electron acceptors, nitrite, oxygen, or hydroxylamine (3,13). Cytochrome cd 1 can act as an oxidase; and in the early stages of this reaction an oxidized state of the protein with His/Met coordination at the c-type cytochrome center has been observed (10,15), as was also the case for a form of the enzyme seen after a 1-electron oxidation of cytochrome cd 1 by nitrite (5). His/Met coordination of the heme of the c domain in the oxidized state is also found in solution for both the semi-apo form of the protein that has lost the d 1 heme (15) and the c domain expressed in isolation (16).…”

mentioning

confidence: 99%

Structure and Kinetic Properties of Paracoccus pantotrophus Cytochrome cd1 Nitrite Reductase with the d1 Heme Active Site Ligand Tyrosine 25 Replaced by Serine

Gordon

Sjögren

Löfqvist

et al. 2003

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

The 1.4-Å crystal structure of the oxidized state of a Y25S variant of cytochrome cd 1 nitrite reductase from Paracoccus pantotrophus is described. It shows that loss of Tyr 25 , a ligand via its hydroxy group to the iron of the d 1 heme in the oxidized (as prepared) wild-type enzyme, does not result in a switch at the c heme of the unusual bishistidinyl coordination to the histidine/methionine coordination seen in other conformations of the enzyme. The Ser 25 side chain is seen in two positions in the d 1 heme pocket with relative occupancies of ϳ7:3, but in neither case is the hydroxy group bound to the iron atom; instead, a sulfate ion from the crystallization solution is bound between the Ser 25 side chain and the heme iron. Unlike the wild-type enzyme, the Y25S mutant is active as a reductase toward nitrite, oxygen, and hydroxylamine without a reductive activation step. It is concluded that Tyr 25 is not essential for catalysis of reduction of any substrate, but that the requirement for activation by reduction of the wild-type enzyme is related to a requirement to drive the dissociation of this residue from the active site. The Y25S protein retains the d 1 heme less well than the wild-type protein, suggesting that the tyrosine residue has a role in stabilizing the binding of this cofactor.

show abstract

Time-resolved Infrared Spectroscopy Reveals a Stable Ferric Heme-NO Intermediate in the Reaction of Paracoccus pantotrophus Cytochrome cd 1 Nitrite Reductase with Nitrite

Cited by 67 publications

References 36 publications

Y25S Variant of Paracoccus pantotrophus Cytochrome cd1 Provides Insight into Anion Binding by d1 Heme and a Rare Example of a Critical Difference between Solution and Crystal Structures

Y25S Variant of Paracoccus pantotrophus Cytochrome cd1 Provides Insight into Anion Binding by d1 Heme and a Rare Example of a Critical Difference between Solution and Crystal Structures

The nitrite reductase from Pseudomonas aeruginosa : Essential role of two active-site histidines in the catalytic and structural properties

Structure and Kinetic Properties of Paracoccus pantotrophus Cytochrome cd1 Nitrite Reductase with the d1 Heme Active Site Ligand Tyrosine 25 Replaced by Serine

Contact Info

Product

Resources

About