TCDB is operated by the Saier Lab Bioinformatics Group

 

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)

 

References associated with 5.A.3 family:

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. 2233673
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.
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. 16236714
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. 7751291
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. 11443088
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. 11884747
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. 14522592
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. 8022286
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. 15716436
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. 2180922
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. 10336636
Richardson, D. and G. Sawers. (2002). Structural biology. PMF through the redox loop. Science 295: 1842-1843. 11884738
Rothery, R.A., G.J. Workun, and J.H. Weiner. (2008). The prokaryotic complex iron-sulfur molybdoenzyme family. Biochim. Biophys. Acta. 1778: 1897-1929. 17964535
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. 18930017
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. 11844760
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. 22081391
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. 9230919
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. 1324728