The prokaryotic complex iron–sulfur molybdoenzyme family

Rothery, Richard A.; Workun, Gregory J.; Weiner, Joël H.

doi:10.1016/j.bbamem.2007.09.002

Cited by 202 publications

(172 citation statements)

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“…Phylogenetic analysis of the three different catalytic subunit A protein sequences placed them in a distinct branch containing dimethyl sulfoxide (DMSO) reductases, which also often have activity towards trimethylamine N-oxide (Supplementary Figure 4). In addition to the genes for subunit A proteins, a gene encoding one copy of a 'four-cluster protein' subunit (subunit B) was identified, whereas no genes were identified for putative homologues of complex iron-sulfur molybdoenzyme subunit C proteins, which typically act as membrane anchors for many multimeric complex iron-sulfur molybdoenzyme complexes (Rothery et al, 2008). Further, twin-arginine translocation translocation signal peptides were not identified for the predicted A or B subunits, and together, suggest that this complex may be cytoplasmic or interacting with other membrane-bound respiratory proteins by unknown mechanisms.…”

Section: Electron Donating and Processing Reactionsmentioning

confidence: 99%

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

et al. 2013

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Bacteria of the class Dehalococcoidia (DEH), phylum Chloroflexi, are widely distributed in the marine subsurface, yet metabolic properties of the many uncultivated lineages are completely unknown. This study therefore analysed genomic content from a single DEH cell designated 'DEH-J10' obtained from the sediments of Aarhus Bay, Denmark. Real-time PCR showed the DEH-J10 phylotype was abundant in upper sediments but was absent below 160 cm below sea floor. A 1.44 Mbp assembly was obtained and was estimated to represent up to 60.8% of the full genome. The predicted genome is much larger than genomes of cultivated DEH and appears to confer metabolic versatility. Numerous genes encoding enzymes of core and auxiliary beta-oxidation pathways were identified, suggesting that this organism is capable of oxidising various fatty acids and/or structurally related substrates. Additional substrate versatility was indicated by genes, which may enable the bacterium to oxidise aromatic compounds. Genes encoding enzymes of the reductive acetyl-CoA pathway were identified, which may also enable the fixation of CO 2 or oxidation of organics completely to CO 2 . Genes encoding a putative dimethylsulphoxide reductase were the only evidence for a respiratory terminal reductase. No evidence for reductive dehalogenase genes was found. Genetic evidence also suggests that the organism could synthesise ATP by converting acetyl-CoA to acetate by substrate-level phosphorylation. Other encoded enzymes putatively conferring marine adaptations such as salt tolerance and organo-sulphate sulfohydrolysis were identified. Together, these analyses provide the first insights into the potential metabolic traits that may enable members of the DEH to occupy an ecological niche in marine sediments.

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Section: Electron Donating and Processing Reactionsmentioning

confidence: 99%

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

et al. 2013

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“…The sulfite oxidase (SO) family, with an LMo-Scysteine residue (-OH/OH 2 ) (=O) core, includes wellknown enzymes such as human SO and plant assimilatory nitrate reductases (NaR, enzymes that catalyse the first and rate-limiting step of nitrate assimilation in plants, algae and fungi), but also the prokaryotic sulfite dehydrogenases [9]. The dimethylsulfoxide reductase (DMSOR) family has an L 2 MoXY core, where X and Y represent terminal =O, -OH, =S, and -SH groups and/or oxygen, sulfur or selenium atoms from cysteine, selenocysteine, serine or aspartate residue side chains [10]. This is a larger and more diverse family, constituted by only prokaryotic enzymes such as the DMSOR and formate dehydrogenase, as well as dissimilatory NaR (periplasmic or membrane-associated b a Scheme 1 The pterin cofactor structure (a) and the proposed mechanism of XO-catalysed hydroxylation (b).…”

Section: Introductionmentioning

confidence: 99%

Nitrite reduction by xanthine oxidase family enzymes: a new class of nitrite reductases

Maia

Moura

2010

J Biol Inorg Chem

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Mammalian xanthine oxidase (XO) and Desulfovibrio gigas aldehyde oxidoreductase (AOR) are members of the XO family of mononuclear molybdoenzymes that catalyse the oxidative hydroxylation of a wide range of aldehydes and heterocyclic compounds. Much less known is the XO ability to catalyse the nitrite reduction to nitric oxide radical (NO). To assess the competence of other XO family enzymes to catalyse the nitrite reduction and to shed some light onto the molecular mechanism of this reaction, we characterised the anaerobic XO-and AORcatalysed nitrite reduction. The identification of NO as the reaction product was done with a NO-selective electrode and by electron paramagnetic resonance (EPR) spectroscopy. The steady-state kinetic characterisation corroborated the XO-catalysed nitrite reduction and demonstrated, for the first time, that the prokaryotic AOR does catalyse the nitrite reduction to NO, in the presence of any electron donor to the enzyme, substrate (aldehyde) or not (dithionite). Nitrite binding and reduction was shown by EPR spectroscopy to occur on a reduced molybdenum centre. A molecular mechanism of AOR-and XO-catalysed nitrite reduction is discussed, in which the higher oxidation states of molybdenum seem to be involved in oxygen-atom insertion, whereas the lower oxidation states would favour oxygenatom abstraction. Our results define a new catalytic performance for AOR-the nitrite reduction-and propose a new class of molybdenum-containing nitrite reductases.

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“…In the equivalent mutant of E. coli DmsABC (DmsA-R61S), quinol:Me 2 SO oxidoreductase activity is also eliminated, but activity with benzyl viologen as donor is retained (50). Comparison of the active site funnels of NarGHI and an enzyme related to DmsABC (Rhodobacter Me 2 SO reductase) reveals that the former enzyme has an unusually narrow active site funnel (4) and that this may prevent electron donation directly to the MobisPGD cofactor.…”

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confidence: 99%

Protein Crystallography Reveals a Role for the FS0 Cluster of Escherichia coli Nitrate Reductase A (NarGHI) in Enzyme Maturation

Rothery

Bertero

Spreter

et al. 2010

Journal of Biological Chemistry

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We have used site-directed mutagenesis, EPR spectroscopy, redox potentiometry, and protein crystallography to monitor assembly of the FS0 [4Fe-4S] cluster and molybdo-bis(pyranopterin guanine dinucleotide) cofactor (Mo-bisPGD) of the Escherichia coli nitrate reductase A (NarGHI) catalytic subunit (NarG). Cys and Ser mutants of NarG-His 49 both lack catalytic activity, with only the former assembling FS0 and Mo-bisPGD. Importantly, both prosthetic groups are absent in the NarG-H49S mutant. EPR spectroscopy of the Cys mutant reveals that the E m value of the FS0 cluster is decreased by at least 500 mV, preventing its participation in electron transfer to the MobisPGD cofactor. To demonstrate that decreasing the FS0 cluster E m results in decreased enzyme activity, we mutated a critical Arg residue (NarG-Arg 94 ) in the vicinity of FS0 to a Ser residue. In this case, the E m of FS0 is decreased by 115 mV, with a concomitant decrease in enzyme turnover to ϳ30% of the wild type. Analysis of the structure of the NarG-H49S mutant reveals two important aspects of NarGHI maturation: (i) apomolybdoNarGHI is able to bind GDP moieties at their respective P and Q sites in the absence of the Mo-bisPGD cofactor, and (ii) a critical segment of residues in NarG, 49 HGVNCTG 55 , must be correctly positioned to ensure holoenzyme maturation.Escherichia coli, when grown anaerobically with nitrate as respiratory oxidant, develops a respiratory chain terminated by a membrane-bound quinol:nitrate oxidoreductase (NarGHI) (1-3). This enzyme is an archetype of the complex iron-sulfur molybdoenzyme (CISM) 2 family (4) that includes E. coli formate dehydrogenase N (FdnGHI (5)), E. coli Me 2 SO reductase (DmsABC (6)), Wolinella succinogenes polysulfide reductase (PsrABC (7, 8)), Salmonella typhymurium thiosulfate reductase (PhsABC (9)), and Salmonella enterica tetrathionate reductase (TtrABC (10)). These enzymes and their close relatives contribute significantly to the remarkable metabolic diversity of bacteria.NarGHI and the other CISM archetypes comprise a mononuclear molybdenum cofactor (molybdo-bis(pyranopterin guanine dinucleotide) (Mo-bisPGD))-containing catalytic subunit, e.g. NarG; a four-cluster protein subunit, e.g. NarH; and a membrane anchor protein, e.g. NarI. Each catalytic subunit contains a [4Fe-4S] cluster in addition to MobisPGD, and many of the membrane anchor subunits are also diheme cytochromes b. The five [Fe-S] clusters are referred to as FS0 -FS4, with increasing distance from Mo-bisPGD, and the entire electron transfer relay (ETR) in NarGHI, including the two hemes, spans a distance of almost 100 Å (2).In NarGHI, Mo-bisPGD provides the site of nitrate reduction at its redox-active molybdenum atom. The molybdenum atom is coordinated by two pyranopterin guanine dinucleotide (PGD) moieties via a bis-dithiolene linkage (11-13). These PGD groups are referred to as the P-and Q-pterins, and they are proximal and distal, respectively, to the FS0 [4Fe-4S] cluster. The bis-dithiolene coordination is supplemented by one oxo gr...

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The prokaryotic complex iron–sulfur molybdoenzyme family

Cited by 202 publications

References 177 publications

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi

Nitrite reduction by xanthine oxidase family enzymes: a new class of nitrite reductases

Protein Crystallography Reveals a Role for the FS0 Cluster of Escherichia coli Nitrate Reductase A (NarGHI) in Enzyme Maturation

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