Insights into heme-based O2 sensing from structure–function relationships in the FixL proteins

Rodgers, Kenton R.; Lukat-Rodgers, Gudrun S.

doi:10.1016/j.jinorgbio.2005.02.016

Cited by 41 publications

(34 citation statements)

References 64 publications

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“…The consequent movement of the iron in the plane of the porphyrin ring triggers a series of conformational changes that inhibit the kinase activity of FixL. There is a great deal of structural and biochemical information for FixL proteins, so the mechanism by which oxygen regulates the kinase activity is quite well understood [31][32][33]. FixL can bind other haem ligands (such as CO and NO) but these do not inhibit the kinase activity, and so their interaction with FixL is probably not physiologically significant.…”

Section: Regulatory Proteinsmentioning

confidence: 99%

Nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors

Spiro

2012

Phil. Trans. R. Soc. B

111

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Several biochemical mechanisms contribute to the biological generation of nitrous oxide (N 2 O). N 2 O generating enzymes include the respiratory nitric oxide (NO) reductase, an enzyme from the flavo-diiron family, and flavohaemoglobin. On the other hand, there is only one enzyme that is known to use N 2 O as a substrate, which is the respiratory N 2 O reductase typically found in bacteria capable of denitrification (the respiratory reduction of nitrate and nitrite to dinitrogen). This article will briefly review the properties of the enzymes that make and consume N 2 O, together with the accessory proteins that have roles in the assembly and maturation of those enzymes. The expression of the genes encoding the enzymes that produce and consume N 2 O is regulated by environmental signals (typically oxygen and NO) acting through regulatory proteins, which, either directly or indirectly, control the frequency of transcription initiation. The roles and mechanisms of these proteins, and the structures of the regulatory networks in which they participate will also be reviewed.

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Section: Regulatory Proteinsmentioning

confidence: 99%

Nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors

Spiro

2012

Phil. Trans. R. Soc. B

111

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“…Because CO can only bind to ferrous heme, the reaction with CO was initiated by adding 5 mM DTT to a 1 lM solution of cyt-c¢-T104C-OG488, saturated with CO. 1 CO binding to cyt-c¢-T104C-OG488 was characterized by a large increase in the absorbance at 418 nm with a rate constant of 1.4 · 10 -2 s -1 , and a second process with a rate constant of 6 · 10 -4 s -1 . 2 Assuming pseudo first-order kinetics [28], the rate constant of the first, major process corresponds to a bimolecular rate constant of 9.8 M -1 s -1 . This is similar to the value obtained for the reaction of CO with wild-type cyt-c¢ ( Fig.…”

Section: Monitoring Ligand-induced Monomerization Using Native Msmentioning

confidence: 99%

“…The binding of diatomic gases such as O 2 , CO or NO to gas-sensing heme proteins illustrates that even the binding of small molecules can cause large rearrangements in a protein's secondary, tertiary or quaternary structure [1]. Binding of O 2 to the regulatory heme-PAS domain of FixL is involved in the regulation of gene expression in nitrogen-fixing bacteria by inactivating the FixL kinase domain [2]. CO binding to the heme of the transcription factor CooA activates its DNA binding domain, initiating the transcription of enzymes that allow the photosynthetic bacterium Rhodospirillum rubrum to grow on CO as a sole energy source [3].…”

Section: Introductionmentioning

confidence: 99%

Ligand-induced monomerization of Allochromatium vinosum cytochrome c′ studied using native mass spectrometry and fluorescence resonance energy transfer

et al. 2007

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Cytochrome c¢ from Allochromatium vinosum is an attractive model protein to study ligand-induced conformational changes. This homodimeric protein dissociates into monomers upon binding of NO, CO or CN -to the iron of its covalently attached heme group. While ligand binding to the heme has been well characterized using a variety of spectroscopic techniques, direct monitoring of the subsequent monomerization has not been reported previously. Here we have explored two biophysical techniques to simultaneously monitor ligand binding and monomerization. Native mass spectrometry allowed the detection of the dimeric and monomeric forms of cytochrome c¢ and even showed the presence of a CO-bound monomer. The kinetics of the ligand-induced monomerization were found to be significantly enhanced in the gas phase compared with the kinetics in solution, however. Ligand binding to the heme and the dissociation of the dimer in solution were also studied using energy transfer from a fluorescent probe to both heme groups of the protein. Comparison of ligand binding kinetics as observed with UV-vis spectroscopy with changes in fluorescence suggested that binding of one CO molecule per dimer could be sufficient for monomerization.

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“…This receptor uses three arginine residues to sense aspartate (2), suggesting that sensing involves electrostatic interactions between ligand and receptor, and one of these arginines was found to be mutated in a recently isolated Tar variant with altered specificity for novel attractants (3). Another intensively studied receptor is the O 2 -sensing heme protein, FixL, of Rhizobia, for which O 2 binding to the permanently bound heme allosterically modifies the activity of the histidine kinase domain (4); in this case, discrimination of dioxygen from other small molecules has been proposed to depend on the ability of a critical arginine residue to hydrogen bond with its target ligand (5). Determinants of specificity in histidine protein kinases that sense macromolecular ligands such as peptides are unknown.…”

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confidence: 99%

“…As a general rule, only the single cognate receptor-ligand interaction results in activation; most heterologous interactions inhibit activation of the receptor, although a few are inert. 4 It is particularly remarkable that a wide variety of thiolactone peptides can inhibit any given receptor competitively, but only a single one can activate it (17).…”

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confidence: 99%

Identification of Ligand Specificity Determinants in AgrC, the Staphylococcus aureus Quorum-sensing Receptor

Geisinger

George

Muir

et al. 2008

Journal of Biological Chemistry

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Activation of the agr system, a major regulator of staphylococcal virulence, is initiated by the binding of a specific autoinducing peptide (AIP) to the extracellular domain of AgrC, a classical receptor histidine protein kinase. There are four known agr specificity groups in Staphylococcus aureus, and we have previously localized the determinant of AIP receptor specificity to the C-terminal half of the AgrC sensor domain. We have now identified the specific amino acid residues that determine ligand activation specificity for agr groups I and IV, the two most closely related. Comparison of the AgrC-I and AgrC-IV sequences revealed a set of five divergent residues in the region of the second extracellular loop of the receptor that could be responsible. Accordingly, we exchanged these residues between AgrC-I and AgrC-IV and tested the resulting constructs for activation by the respective AIPs, measuring activation kinetics with a transcriptional fusion of blaZ to the principal agr promoter, P3. Exchange of all five residues caused a complete switch in receptor specificity. Replacement of two of the AgrC-IV residues by the corresponding residues in AgrC-I caused the receptor to be activated by AIP-I nearly as well as the wild type AgrC-I receptor. Replacement of two different AgrC-I residues by the corresponding AgrC-IV residues broadened receptor recognition specificity to include both AIPs. Various types of intermediate activity were observed with other replacement mutations. Preliminary characterization of the AgrC-I-AIP-I interaction suggests that ligand specificity may be sterically determined.

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Insights into heme-based O2 sensing from structure–function relationships in the FixL proteins

Cited by 41 publications

References 64 publications

Nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors

Nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors

Ligand-induced monomerization of Allochromatium vinosum cytochrome c′ studied using native mass spectrometry and fluorescence resonance energy transfer

Identification of Ligand Specificity Determinants in AgrC, the Staphylococcus aureus Quorum-sensing Receptor

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