5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family

Bacterial genomes encode an extensive range of respiratory enzymes that enable respiratory metabolism with a diverse group of reducing and oxidizing substrates under both aerobic and anaerobic growth conditions. An important class of enzymes is the complex iron-sulfur molybdoenzyme (CISM) family (Rothery et al., 2008). This class consists of the following subunits. (i) A molybdo-bis(pyranopterin guanine dinucleotide) (Mo-bisPGD) cofactor-containing catalytic subunit that also contains a cubane [Fe-S] cluster (FS0). (ii) A four-cluster protein (FCP) subunit that contains 4 cubane [Fe-S] clusters (FS1-FS4). (iii) A membrane anchor protein (MAP) subunit which anchors the catalytic and FCP subunits to the cytoplasmic membrane. Rothery et al. (2008) define the CISM family of enzymes on the basis of emerging structural and bioinformatic data, and show that the catalytic and FCP subunit architectures appear in a wide range of bacterial redox enzymes. They evaluate evolutionary events involving genes encoding the CISM catalytic subunit that resulted in the emergence of the complex I (NADH:ubiquinone oxidoreductase) Nqo3/NuoG subunit architecture. They also trace a series of evolutionary events leading from a primordial Cys-containing peptide to the FCP architecture. Finally, many of the CISM archetypes and related enzymes rely on the tat translocon to transport fully folded monomeric or dimeric subunits across the cytoplasmic membrane.

The membrane-bound nitrate reductase-A (NR-A) (NarGHI; α2β2γ4, β, and γ in E. coli; also called NR-1) employs a redox loop to couple quinol oxidation to the equivalent of proton translocation, thereby generating a proton motive force (pmf) during anaerobic respiration. In this process, ubiquinol oxidation by the cytochrome b subunit (NarI) occurs at the periplasmic side of the membrane, releasing two protons, and nitrate reduction by NarG occurs in the cytoplasm, consuming two protons to form water. There is therefore a net loss of H+ in the cytoplasm and a net gain of H+ in the periplasm with transmembrane electron flow from the periplasm to the cytoplasm, generating a pmf, negative inside (Rothery et al., 2007).

NarGHI contains Mo-molybdopterin guanine dinucleotide, FMN(H2), selenocysteine, five iron-sulfur centers and diheme cytochrome b556. The enzyme is strongly inhibited by azide (N3-). Synthesis is maximal during anaerobic growth in the presence of nitrate. The α-subunit (NarG; 1247 aas) is the site of NO3- reduction to NO2-. The molybdenum cofactor, selenocysteine, FMNH2 and one iron-sulfur center are all present in NarG. The NarH (β) subunit (512 aas) contains four more iron sulfur centers. The NarI (γ) subunit (225 aas; 5 putative TMSs) is the integral membrane b-type cytochrome that anchors the α and β subunits to the membrane on the cytoplasmic side and oxidizes quinol on the periplasmic side (Jormakka et al., 2002; Rothery et al., 2007).

Like NR-A, formate dehydrogenase (FDH) is a three subunit enzyme (FdnGHI) homologous to nitrate reductase-A. It has an α2β2γ 4 subunit composition and contains the same cofactors as does nitrate reductase. The dehydrogenase transfers an electron pair across the membrane from formate (in) to quinone (out). It probably uses the same mechanism as that described above for nitrate reductase.

The soluble α-subunits of NR-A and FDH are homologous to the α-subunits of other soluble molybdo-cofactor proteins such as DMSO reductase, TMAO reductase, biotin sulfoxide reductase and thiosulfate reductase. The soluble β-subunits of NR-A and FDH show some sequence similarity to subunit F of the tungstate-containing formyl methanofuran dehydrogenase of Methanobacterium thermoautotrophicum (TC #3.D.8.1.1). Additionally they are homologous to β-subunits of the oxidoreductases cited above plus selenate reductase, tetrathionate reductase, polysulfide reductase, hydrogenases, carbon monoxide reductase, ferridoxin, polyferridoxin, etc. The NarI (γ) subunit is more sequence divergent than the α or β subunits but is homologous to a subunit in the archaeal heterodisulfide reductase (TC #3.D.7). The FdnI (γ) subunit of FDH has 4 predicted TMSs in contrast to NarI which has 5. The NarJ protein (P11351, sometimes called the δ-subunit) is required for assembly of the NR-cytochrome b complex.

The net overall reaction catalyzed by NR-A is probably:

nitrate (NO3-) (in) + quinol (out) + 2H+ (in) → nitrite (NO2-) (in) + quinone (out)
+ 2H+ (out) + H20 (in).

The overall reaction catalyzed by formate dehydrogenase is probably:

formate (HCO2-) (in) + quinone (out) + 2H+ (out) → CO2 (in) + quinol (out) + H+ (in).

The net transmembrane electron transfer reactions for NR-A and FDH, and probably other homologous enzymes are:

(a) 2e- (out) → 2e- (in) (NR-A)

(b) 2e- (in) → 2e- (out) (FDH)



This family belongs to the .

 

References:

Blasco, F., C. Iobbi, J. Ratouchniak, V. Bonnefoy, and M. Chippaux. (1990). Nitrate reductases of Escherichia coli: sequence of the second nitrate reductase and comparison with that encoded by the narGHJI operon. Mol. Gen. Genet. 222: 104-111.

Dhouib, R., D.S. Othman, V. Lin, X.J. Lai, H.G. Wijesinghe, A.T. Essilfie, A. Davis, M. Nasreen, P.V. Bernhardt, P.M. Hansbro, A.G. McEwan, and U. Kappler. (2016). A Novel, Molybdenum-Containing Methionine Sulfoxide Reductase Supports Survival of in an Model of Infection. Front Microbiol 7: 1743.

Gennis, R.B. and V. Stewart. (1996). Respiration. In F.C. Neidhardt et al. (eds), Escherichia coli and Salmonella. Cellular and Molecular Biology, 2nd ed. Washington, DC: ASM Press, pp. 217-261.

Ghosh, S. and A. Bagchi. (2015). Comparative analysis of the mechanisms of sulfur anion oxidation and reduction by dsr operon to maintain environmental sulfur balance. Comput Biol Chem 59PtA: 177-184.

Gon, S., J.C. Patte, V. Méjean, and C. Iobbi-Nivol. (2000). The torYZ (yecK bisZ) operon encodes a third respiratory trimethylamine N-oxide reductase in Escherichia coli. J. Bacteriol. 182: 5779-5786.

Guiral, M., P. Tron, C. Aubert, A. Gloter, C. Iobbi-Nivol, and M.T. Giudici-Orticoni. (2005). A membrane-bound multienzyme, hydrogen-oxidizing, and sulfur-reducing complex from the hyperthermophilic bacterium Aquifex aeolicus. J. Biol. Chem. 280: 42004-42015.

Heinzinger, N.K., S.Y. Fujimoto, M.A. Clark, M.S. Moreno, and E.L. Barrett. (1995). Seqence analysis of the phs operon in Salmonella typhimurium and the contribution of thiosulfate reduction to anaerobic energy metabolism. J. Bacteriol. 177: 2813-2820.

Johnson, H.A., D.A. Pelletier, and A.M. Spormann. (2001). Isolation and characterization of anaerobic ethylbenzene dehydrogenase, a novel Mo-Fe-S enzyme. J Bacteriol. 183: 4536-4542.

Jormakka, M., S. Tornroth, B. Byrne, and S. Iwata. (2002). Molecular basis of proton motive force generation: structure of formate dehydrogenase-N. Science 295: 1863-1868.

Lubitz, S.P. and J.H. Weiner. (2003). The Escherichia coli ynfEFGHI operon encodes polypeptides which are paralogues of dimethyl sulfoxide reductase (DmsABC). Arch. Biochem. Biophys. 418: 205-216.

Mejean, V., C. Iobbi-Nivol, M. Lepelletier, G. Giordano, M. Chippaux, and M.C. Pascal. (1994). TMAO anaerobic respiration in Escherichia coli: involvement of the tor operon. Mol. Microbiol. 11: 1169-1179.

Müller, J.A. and S. DasSarma. (2005). Genomic analysis of anaerobic respiration in the archaeon Halobacterium sp. strain NRC-1: dimethyl sulfoxide and trimethylamine N-oxide as terminal electron acceptors. J. Bacteriol. 187: 1659-1667.

Pereira, P.M., M. Teixeira, A.V. Xavier, R.O. Louro, and I.A. Pereira. (2006). The Tmc complex from Desulfovibrio vulgaris hildenborough is involved in transmembrane electron transfer from periplasmic hydrogen oxidation. Biochemistry 45: 10359-10367.

Pierson, D.E. and A. Campbell. (1990). Cloning and nucleotide sequence of bisC, the structural gene for biotin sulfoxide reductase in Escherichia coli. J. Bacteriol. 172: 2194-2198.

Rhee, S.K. and G. Fuchs. (1999). Phenylacetyl-CoA:acceptor oxidoreductase, a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 262: 507-515.

Richardson, D. and G. Sawers. (2002). Structural biology. PMF through the redox loop. Science 295: 1842-1843.

Rothery, R.A., G.J. Workun, and J.H. Weiner. (2008). The prokaryotic complex iron-sulfur molybdoenzyme family. Biochim. Biophys. Acta. 1778: 1897-1929.

Saier, M.H., Jr. (1987). Enzymes in Metabolic Pathways. A Comparative Study of Mechanism, Structure, Evolution, and Control. New York, NY: Harper and Row.

Simon, J., R.J. van Spanning, and D.J. Richardson. (2008). The organisation of proton motive and non-proton motive redox loops in prokaryotic respiratory systems. Biochim. Biophys. Acta. 1777: 1480-1490.

Stewart, V., Y. Lu, and A.J. Darwin. (2002). Periplasmic nitrate reductase (NapABC enzyme) supports anaerobic respiration by Escherichia coli K-12. J. Bacteriol. 184: 1314-1323.

Stoffels L., Krehenbrink M., Berks BC. and Unden G. (2012). Thiosulfate reduction in Salmonella enterica is driven by the proton motive force. J Bacteriol. 194(2):475-85.

Unden, G. and J. Bongaerts. (1997). Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochim. Biophys. Acta 1320: 217-234.

Weiner, J.H., R.A. Rothery, D. Sambasivarao, and C.A. Trieber. (1992). Molecular analysis of dimethylsulfoxide reductase: a complex iron-sulfur molybdoenzyme of Escherichia coli. Biochim. Biophys. Acta 1102: 1-18.

Examples:

TC#NameOrganismal TypeExample
5.A.3.1.1

Anaerobic, respiratory, membrane-bound nitrate reductase, NarGHI. Two protons are consumed in the cytoplasm while two protons are released in the periplasm, contributing to the pmf (Simon et al., 2008).

Bacteria and archaea

NarGHI of E. coli
NarG (α)
NarH (β)
NarI (γ)

 
5.A.3.1.2Anaerobic, respiratory, membrane-bound nitrate reductase, NarZYV (Blasco et al., 1990)BacteriaNarZYV of E. coli
NarZ(α) P19319
NarY(β) P19318
NarV(γ) P19316
 
Examples:

TC#NameOrganismal TypeExample
5.A.3.10.1Tetrathionate reductase, TtrABCBacteriaTtrABC of Bordetella bronchiseptica
TtrA (α) (NP_887789)
TtrB (β) (NP_887791)
TtrC (γ) (NP_887790)
 
Examples:

TC#NameOrganismal TypeExample
5.A.3.11.1Phenylacetyl-CoA:acceptor oxidoreductase (Rhee and Fuchs, 1999)BacteriaPadB2C2D of Azoarcus sp. EbN1
PadB2 (α) CAI09327
PadC2 (β) CAI09328
PadD (γ) CAI09186
 
5.A.3.11.2The cytoplasmic sulfur/tetrathionate/polysulfide oxidoreductase, SreABC (Guiral et al., 2005) [While SreA and B most resemble 5.A.3.11.1, SreC most resembles 5.A.3.3.2.]BacteriaSreABC of Aquifex aeolicus
SreA (α) (AAC07243)
SreB (β) (AAC07244)
SreC (γ) (AAC07245)
 
Examples:

TC#NameOrganismal TypeExample
5.A.3.2.1

Anaerobic, respiratory, membrane-bound formate dehydrogenase, FdnGHI. Two protons are consumed in the cytoplasm while two protons are released in the periplasm, contributing to the pmf (Simon et al., 2008).

Bacteria and archaea

FdnGHI of E. coli
FdnG (α)
FdnH (β)
FdnI (γ)

 
Examples:

TC#NameOrganismal TypeExample
5.A.3.3.1Anaerobic dimethylsulfoxide (DMSO) reductase, (YnfEFGH) (Weiner et al., 1992; Lubitz and Weiner, 2003)BacteriaYnfEFGH of E. coli
YnfE(α or A chain) (reductase) (P77374)
YnfF (α or A chain) (reductase) (P77783)
YnfG (β or B chain) (electron transfer protein) (P0AAJ1)
YnfH (γ or C chain) (membrane anchor protein) (P76173)
 
5.A.3.3.2Anaerobic dimethyl sulfoxide (DMSO) reductase, DmsABC (Lubitz and Weiner, 2003)BacteriaDmsABC of E. coli
DmsA(α) P18775
DmsB(β) P18776
DmsC(γ) P18777
 
5.A.3.3.3

Anaerobic dimethylsulfoxide (DMSO)/trimethylamine-N-oxide (TMAO) reductase (Müller and DasSarma, 2005)

Archaea

DmsABCE of Halobacterium sp. strain NRC-1
DmsA (α) (AAG19284)
DmsC (β) (AAG19286)
DmsB (γ1) (AAG19285)
DmsE (γ2 (AAG19283)

 
Examples:

TC#NameOrganismal TypeExample
5.A.3.4.1Anaerobic trimethylamine-N-oxide (TMAO) reductase 1, TorAC (Mejean et al., 1994)BacteriaTorAC of E. coli
TorA (α) (precursor 1) (P33225)
TorC (cytochrome c-type protein) (P33226)
 
5.A.3.4.2

Periplasmic anaerobic trimethylamine-N-oxide reductase 2, TorYZ (also called YecK/BisZ) (Gon et al. 2000). It also reduces biotin sulfoxide and other N- and S-oxides, but less efficiency that TMAO.

Bacteria

TorYZ of E. coli
TorY (cytochrome c-type protein) (P52005)
TorZ (α) (P58362)

 
5.A.3.4.3Biotin d-sulfoxide reductase, BisC (requires a small thioredoxin-like protein) (Pierson and Campbell, 1990)BacteriaBisC of E. coli
BisC (α) (P20099)
 
5.A.3.4.4

Periplasmic anaerobic methionine oxide reductase 2, TorYZ (also called MtsZ/BisC), both with an N-terminal TMS. It supports survival of Haemophilus influenzae in an in vivo model of infection (Dhouib et al. 2016). It is an S- and N-oxide reductase with a stereospecificity for S-sulfoxides. The enzyme converts two physiologically relevant sulfoxides, biotin sulfoxide (BSO) and methionine sulfoxide (MetSO), with the kinetic parameters suggesting that MetSO is the natural substrate of this enzyme (Dhouib et al. 2016).

TorYZ of Haemophilus influenzae

 
Examples:

TC#NameOrganismal TypeExample
5.A.3.5.1

Thiosulfate reductase, PhsABC (Heinzinger et al., 1995). Menaquinone is the sole electron donor. The endoergonic reduction reaction is driven by the pmf by a reverse loop mechanism. The enzyme can catalyze oxidation of sulfide to sulfite and sulfite to thiosulfate in an exergonic reaction that is pmf-independent (Stoffels et al., 2011).

Bacteria

PhsABC of Salmonella typhimurium
PhsA (α) (molybdopterin subunit) (P37600)
PhsB (β) (reductase) (P0A1I1)
PhsC (γ) (cytochrome b subunit) (P37602)

 
5.A.3.5.2Polysulfide reductase, PsrABCBacteriaPsrABC of Wolinella succinogenes
PsrA (α or chain A) (P31075)
PsrB (β or chain B) (P31076)
PsrC (γ or chain C) (P31077)
 
Examples:

TC#NameOrganismal TypeExample
5.A.3.6.1Arsenite oxidase, AoxABBacteriaAoxAB of Alcaligenes faecalis
AoxB (α) (AOI) (Q7SIF4)
AoxA (β) (AOII) (Q7SIF3)
 
Examples:

TC#NameOrganismal TypeExample
5.A.3.7.1Pyrogallol hydroxytransferase, AthL/BthLBacteriaAthL/BthL of Pelobacter acidigallici
AthL (α) (P80563)
BthL (β) (P80564)
 
Examples:

TC#NameOrganismal TypeExample
5.A.3.8.1Selenate reductase, SerABCBacteriaSerABC of Thauera selenatis
SerA (α) (Q9S1H0)
SerB (β) (Q9S1G9
SerC (γ) (Q9S1G7)
 
5.A.3.8.2Chlorate reductase, ClrABCBacteriaClrABC of Ideonella dechloratans
ClrA (α) (P60068)
ClrB (β) (P60069)
ClrC (γ) (P60000)
 
Examples:

TC#NameOrganismal TypeExample
5.A.3.9.1Anaerobic ethylbenzene dehydrogenase, EbdABC (Johnson et al., 2001)BacteriaEbdABC in Azoarcus sp EB1
EbdA (α or A-chain) (AAK76387)
EbdB (β or B-chain) (AAK76388
EbdC (γ or C-chain) (AAK76389)