The high resolution crystal structure of DMSO reductase in complex with DMSO 1 1Edited by D. C. Rees

McAlpine, A. S.; McEwan, Alastair G.; Bailey, Susan

doi:10.1006/jmbi.1997.1513

Cited by 162 publications

(205 citation statements)

References 26 publications

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“…Because the two high resolution NapA structures apparently give a consensus for a des-oxo Mo 6ϩ state, they can be set apart from other Mo-bis-MGD reductases such as the membranebound nitrate reductase, dimethyl sulfoxide reductase, and trimethylamine N-oxide reductase, all of which have one or more oxo groups in at least one of the Mo 6ϩ structural states resolved by x-ray crystallography (3,37,54,55). However, two separate extended x-ray absorption fine structure studies on the heterodimeric NapAB of P. pantotrophus have given strong evidence for oxo group ligation in the Mo 6ϩ state (8,41).…”

Section: Figure 3 Spectropotentiometric Properties Of the Momentioning

confidence: 99%

Spectropotentiometric and Structural Analysis of the Periplasmic Nitrate Reductase from Escherichia coli

Jepson¹,

Mohan

Clarke³

et al. 2007

Journal of Biological Chemistry

105

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The Escherichia coli NapA (periplasmic nitrate reductase) contains a [4Fe-4S] cluster and a Mo-bis-molybdopterin guanine dinucleotide cofactor. The NapA holoenzyme associates with a di-heme c-type cytochrome redox partner (NapB). These proteins have been purified and studied by spectropotentiometry, and the structure of NapA has been determined. In contrast to the well characterized heterodimeric NapAB systems of ␣-proteobacteria, such as Rhodobacter sphaeroides and Paracoccus pantotrophus, the ␥-proteobacterial E. coli NapA and NapB proteins purify independently and not as a tight heterodimeric complex. This relatively weak interaction is reflected in dissociation constants of 15 and 32 M determined for oxidized and reduced NapAB complexes, respectively. The surface electrostatic potential of E. coli NapA in the apparent NapB binding region is markedly less polar and anionic than that of the ␣-proteobacterial NapA, which may underlie the weaker binding of NapB. The molybdenum ion coordination sphere of E. coli NapA includes two molybdopterin guanine dinucleotide dithiolenes, a protein-derived cysteinyl ligand and an oxygen atom. The Mo-O bond length is 2.6 Å , which is indicative of a water ligand. The potential range over which the Mo 6؉ state is reduced to the Mo 5؉ state in either NapA (between ؉100 and ؊100 mV) or the NapAB complex (؊150 to ؊350 mV) is much lower than that reported for R. sphaeroides NapA (midpoint potential Mo 6؉/5؉ > ؉350 mV), and the form of the Mo 5؉ EPR signal is quite distinct. In E. coli NapA or NapAB, the Mo 5؉ state could not be further reduced to Mo 4؉. We then propose a catalytic cycle for E. coli NapA in which nitrate binds to the Mo 5؉ ion and where a stable des-oxo Mo 6؉ species may participate.Bacterial nitrate reductases are molybdoenzymes that catalyze the two-electron reduction of nitrate to nitrite. They can be classified into three groups according to their localization and function, namely membrane-bound respiratory, periplasmic respiratory, or cytoplasmic assimilatory enzymes (1, 2). Bacterial respiratory membrane-bound nitrate reductases, such as Escherichia coli NarGHI, are generally integral membrane protein complexes that have an active site on the cytoplasmic face of the membrane and couple quinol oxidation by nitrate to the generation of a transmembrane proton electrochemical gradient (2). The catalytic subunit, NarG, contains a Mo-bis-molybdopterin guanine dinucleotide (Mo-bis-MGD) 3 cofactor and a [4Fe-4S] cluster (3, 4). Periplasmic nitrate reductases (Nap) are also linked to quinol oxidation in respiratory electron transport chains, but do not conserve the free energy of the QH 2 -nitrate couple. Nitrate reduction via Nap can be coupled to energy conservation if the primary quinone reductase, for example NADH dehydrogenase or formate dehydrogenase, generates a proton electrochemical gradient. Thus Nap systems have a range of physiological functions that include the disposal of reducing equivalents during aerobic growth on reduced carbon substrates and anaerob...

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Section: Figure 3 Spectropotentiometric Properties Of the Momentioning

confidence: 99%

Spectropotentiometric and Structural Analysis of the Periplasmic Nitrate Reductase from Escherichia coli

Jepson¹,

Mohan

Clarke³

et al. 2007

Journal of Biological Chemistry

105

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“…The structures of monomeric NapA have been described from E. coli (Jepson et al, 2007) and of the NapAB heterodimer from Rhodobacter sphaeroides (Arnoux et al, 2003). In addition to the Mo-bis-MGD chelates and combinations of oxo (O 22 , OH 2 /H 2 O)-and/or sulfido (S 22 , SH 2 )-based ligands, the coordination sphere of each mononuclear Mo enzyme of the DMSO reductase family is completed by donor atoms derived from serine [TMAO reductase and DMSO reductase (Czjzek et al, 1998;Li et al, 2000;McAlpine et al, 1998)] or cysteine [NAP (Arnoux et al, 2003;Dias et al, 1999;Jepson et al, 2007;Najmudin et al, 2008)]. …”

Section: Introductionmentioning

confidence: 99%

The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB

2010

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In the bacterial periplasm, the reduction of nitrate to nitrite is catalysed by a periplasmic nitrate reductase (NAP) system, which is a species-dependent assembly of protein subunits encoded by the nap operon. The reduction of nitrate catalysed by NAP takes place in the 90 kDa NapA subunit, which contains a Mo-bis-molybdopterin guanine dinucleotide cofactor and one [4Fe"4S] iron-sulfur cluster. A review of the nap operons in the genomes of 19 strains of Shewanella shows that most genomes contain two nap operons. This is an unusual feature of this genus. The two NAP isoforms each comprise three isoform-specific subunits -NapA, a di-haem cytochrome NapB, and a maturation chaperone NapD -but have different membrane-intrinsic subunits, and have been named NAP-a (NapEDABC) and NAP-b (NapDAGHB). Sixteen Shewanella genomes encode both NAP-a and NAP-b. The genome of the vigorous denitrifier Shewanella denitrificans OS217 encodes only NAP-a and the genome of the respiratory nitrate ammonifier Shewanella oneidensis MR-1 encodes only NAP-b. This raises the possibility that NAP-a and NAP-b are associated with physiologically distinct processes in the environmentally adaptable genus Shewanella. IntroductionSpecies of the genus Shewanella are defined as pink-or salmon-coloured, Gram-negative, rod-shaped, facultative anaerobic bacteria with a single polar flagellum that are oxidase-and catalase-positive and can reduce trimethylamine N-oxide (TMAO) and nitrate (Venkateswaran et al., 1999). Almost all Shewanella species to date have been discovered in extreme aquatic or terrestrial environments, including deep-sea trench sediments, Antarctic ice cores, and sites contaminated with toxic compounds, including arsenic, remnants of military explosives or crude oil (Konstantinidis et al., 2009;Zhao et al., 2005Zhao et al., , 2006. Most Shewanella species are classifiable into one or more selected extremophilic subgroups: halophiles, psychrophiles or barophiles (Fredrickson et al., 2008;Hau & Gralnick, 2007;Pakchung et al., 2006). Most recently, Shewanella vesiculosa sp. nov. and Shewanella marina sp. nov. have been characterized from marine environments (Bozal et al., 2009;Park et al., 2009) and contribute to the 51 species of Shewanella identified at the time of writing (http://www.bacterio.cict.fr/). Some Shewanella species, most notably Shewanella oneidensis MR-1, can grow via the reduction of metal oxides -including Fe(III), Mn(IV), Cr(VI), U(VI), Tc(VI), V(V) -thiosulfate, elemental sulfur and arsenate (Burns & DiChristina, 2009;Carpentier et al., 2005;Konstantinidis et al., 2009;Malasarn et al., 2008;Murphy & Saltikov, 2007;Nealson & Saffarini, 1994;Nealson & Little, 1997). The respiratory versatility of Shewanella species has significant implications in bioremediation and in the assembly of microbial fuel cells (Fredrickson et al., 2008;Hou et al., 2009;Kim et al., 2002;Tiedje, 2002). Interest in the ecology and physiology of Shewanella at the genetic level is reflected by the 19 genome sequencing projects completed by the US ...

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“…1a) (1)(2)(3). Although the recent proliferation of x-ray crystal structures for mononuclear molybdenum enzymes has revealed a common structure for the molybdopterin cofactor, they have also revealed considerable diversity in the molybdenum coordination environment (2)(3)(4)(5)(6)(7)(8)(9)(10)(11). However, on the basis of the available crystallographic, spectroscopic, primary sequence, and cyanide inhibition data, these enzymes can be divided into three large families (Fig.…”

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confidence: 99%

“…In one of the two R. capsulatus Me 2 SO reductase x-ray structures, the oxidized form comprises a di-oxo-Mo(VI) center with one of the molybdopterin dithiolates fully dissociated (4). In the other set of R. capsulatus Me 2 SO reductase x-ray structures, the active site is refined as being 7-coordinate in both the oxidized and dimethyl sulfide (ME 2 S)-reduced forms, with both molybdopterin dithiolates attached, in addition to serinate and a spectator oxo group (5,6). There is also an exchangeable terminal oxygen ligand (oxo or hydroxo) that is lengthened (1.8 Å in the x-ray structure (5) and 1.9 Å by EXAFS (20)) compared with a typical terminal MoϭO group (1.7 Å) due to hydrogen bonding to a tryptophan residue, and it is this oxo group that constitutes the site of attack by Me 2 S (5,6,20).…”

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confidence: 99%

Resonance Raman Characterization of Biotin Sulfoxide Reductase

Garton

Temple

Dhawan

et al. 2000

Journal of Biological Chemistry

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Resonance Raman spectroscopy has been used to define active site structures for oxidized Mo(VI) and reduced Mo(IV) forms of recombinant Rhodobacter sphaeroides biotin sulfoxide reductase expressed in Escherichia coli. On the basis of 18 With the exception of nitrogenase, molybdenum enzymes catalyze formal oxygen atom transfer between water and substrate and contain an active site in which the molybdenum is coordinated by the dithiolene side chain of one or two molybdopterins (Fig. 1a) (1-3). Although the recent proliferation of x-ray crystal structures for mononuclear molybdenum enzymes has revealed a common structure for the molybdopterin cofactor, they have also revealed considerable diversity in the molybdenum coordination environment (2-11). However, on the basis of the available crystallographic, spectroscopic, primary sequence, and cyanide inhibition data, these enzymes can be divided into three large families (Fig. 1b) (1). Hydroxylases, such as Desulfovibrio gigas aldehyde oxidoreductase, xanthine oxidase, and xanthine dehydrogenase, represent the xanthine oxidase family, characterized by a Mo(VI) active site with a single molybdopterin, as well as terminal oxo and sulfido groups. The oxotransferase class of molybdoenzymes catalyzes direct oxygen atom transfer between substrate and water and can be divided into two families. The sulfite oxidase family, as represented by sulfite oxidase and assimilatory nitrate reductase, contains Mo(VI) ligated by two oxo groups in addition to a single molybdopterin and a cysteine residue. The dimethyl sulfoxide (Me 2 SO) reductase family comprises mono-oxoMo(VI) sites ligated by two molybdopterins and a protein side chain ligand such as serine, cysteine, or selenocysteine. In addition to Me 2 SO reductase, this family also includes formate dehydrogenase, dissimilatory nitrate reductase, and biotin sulfoxide (BSO) 1 reductase. BSO reductase is found in bacterial systems, such as Rhodobacter sphaeroides and Escherichia coli, and catalyzes the reduction of d-biotin d-sulfoxide to d-biotin (Fig. 2). Although the precise role for BSO reductase in bacterial metabolism has yet to be defined, potential physiological functions include scavenging biotin sulfoxide from the environment, reducing bound intracellular biotin that has become oxidized in an aerobic environment, and protecting the cell from oxidative damage (12). Extensive characterization of this enzyme has been limited due to the low natural abundance of the protein and its constitutive expression (13). However, R. sphaeroides BSO reductase has recently been heterologously expressed in E. coli and characterized as containing the molybdopterin guanine dinucleotide form of the molybdopterin cofactor (14). Using either reduced methyl viologen or NADPH as electron donor, the enzyme was found to exhibit broad substrate specificity and was able to catalyze reduction of nicotinamide-N-oxide, methionine sulfoxide, trimethylamine-N-oxide, and dimethyl sulfoxide with varying efficiencies, in addition to the reduction of biotin ...

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The high resolution crystal structure of DMSO reductase in complex with DMSO 1 1Edited by D. C. Rees

Cited by 162 publications

References 26 publications

Spectropotentiometric and Structural Analysis of the Periplasmic Nitrate Reductase from Escherichia coli

Spectropotentiometric and Structural Analysis of the Periplasmic Nitrate Reductase from Escherichia coli

The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB

Resonance Raman Characterization of Biotin Sulfoxide Reductase

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