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 Iron-Sulfur Protein (ISP) Superfamily.
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|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.|
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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
|5.A.3.1.2||Anaerobic, respiratory, membrane-bound nitrate reductase, NarZYV (Blasco et al., 1990)||Bacteria||NarZYV of E. coli|
|5.A.3.10.1||Tetrathionate reductase, TtrABC||Bacteria||TtrABC of Bordetella bronchiseptica |
TtrA (α) (NP_887789)
TtrB (β) (NP_887791)
TtrC (γ) (NP_887790)
Tetrathionate reductase, subunit A of 1173 aas and up to 4 TMSs, 2 TMSs N-terminal and 2 TMSs in the middle of the protein.
Tetrathionate reductase of Pyrobaculum aerophilum
|5.A.3.11.1||Phenylacetyl-CoA:acceptor oxidoreductase (Rhee and Fuchs, 1999)||Bacteria||PadB2C2D of Azoarcus sp. EbN1 |
PadB2 (α) CAI09327
PadC2 (β) CAI09328
PadD (γ) CAI09186
|5.A.3.11.2||The 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.]||Bacteria||SreABC of Aquifex aeolicus |
SreA (α) (AAC07243)
SreB (β) (AAC07244)
SreC (γ) (AAC07245)
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
|5.A.3.3.1||Anaerobic dimethylsulfoxide (DMSO) reductase, (YnfEFGH) (Weiner et al., 1992; Lubitz and Weiner, 2003)||Bacteria||YnfEFGH 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.3.3.2||Anaerobic dimethyl sulfoxide (DMSO) reductase, DmsABC (Lubitz and Weiner, 2003)||Bacteria||DmsABC of E. coli|
Anaerobic dimethylsulfoxide (DMSO)/trimethylamine-N-oxide (TMAO) reductase (Müller and DasSarma, 2005)
DmsABCE of Halobacterium sp. strain NRC-1
DmsA (α) (AAG19284)
DmsC (β) (AAG19286)
DmsB (γ1) (AAG19285)
DmsE (γ2 (AAG19283)
|5.A.3.4.1||Anaerobic trimethylamine-N-oxide (TMAO) reductase 1, TorAC (Mejean et al., 1994)||Bacteria||TorAC of E. coli |
TorA (α) (precursor 1) (P33225)
TorC (cytochrome c-type protein) (P33226)
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.
TorYZ of E. coli
TorY (cytochrome c-type protein) (P52005)
TorZ (α) (P58362)
|5.A.3.4.3||Biotin d-sulfoxide reductase, BisC (requires a small thioredoxin-like protein) (Pierson and Campbell, 1990)||Bacteria||BisC of E. coli |
BisC (α) (P20099)
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
Thiosulfate reductase, PhsABC (Heinzinger et al., 1995) (Clark and Barrett 1987). Menaquinone is the sole electron donor. The endoergonic reduction reaction is driven by the pmf by a reverse loop mechanism (Stoffels et al. 2012). The enzyme can catalyze oxidation of sulfide to sulfite and sulfite to thiosulfate in an exergonic reaction that is pmf-independent (Stoffels et al. 2012). Because the endoergonic reaction is dependent on the pmf, there may be a proton channels in the complex, (possibly subunit C) that allows proton flux into the cell, coupled to the reduction reaction.
PhsABC of Salmonella typhimurium
PhsA (α) (molybdopterin subunit; 758 aas and 1 - 3 TMSs) (P37600)
PhsB (β) (cytochrome b reductase; 192 aas) (P0A1I1)
PhsC (γ) (cytochrome b subunit; 254 aas and 5 TMSs in a 1 + 2 + 2 TMS arrangement) (P37602)
|5.A.3.5.2||Polysulfide reductase, PsrABC||Bacteria||PsrABC of Wolinella succinogenes |
PsrA (α or chain A) (P31075)
PsrB (β or chain B) (P31076)
PsrC (γ or chain C) (P31077)
Nitrite reductase complex, NrfABCD with subunits: NrfA, 478 aas and 1 N-terminal TMS, P0ABK9; NrfB or YjcI, 188 aas and 1 N-terminal TMS, P0ABL1; NrfC or YjcJ, 223 aas and 1 N-terminal TMS, P0AAK7; NrfD or YjcK, 318 aas and 8 TMSs, P32709.
NrfABCD of E. coli
|5.A.3.6.1||Arsenite oxidase, AoxAB||Bacteria||AoxAB of Alcaligenes faecalis |
AoxB (α) (AOI) (Q7SIF4)
AoxA (β) (AOII) (Q7SIF3)
|5.A.3.7.1||Pyrogallol hydroxytransferase, AthL/BthL||Bacteria||AthL/BthL of Pelobacter acidigallici |
AthL (α) (P80563)
BthL (β) (P80564)
|5.A.3.8.1||Selenate reductase, SerABC||Bacteria||SerABC of Thauera selenatis |
SerA (α) (Q9S1H0)
SerB (β) (Q9S1G9
SerC (γ) (Q9S1G7)
|5.A.3.8.2||Chlorate reductase, ClrABC||Bacteria||ClrABC of Ideonella dechloratans |
ClrA (α) (P60068)
ClrB (β) (P60069)
ClrC (γ) (P60000)
|5.A.3.9.1||Anaerobic ethylbenzene dehydrogenase, EbdABC (Johnson et al., 2001)||Bacteria||EbdABC in Azoarcus sp EB1 |
EbdA (α or A-chain) (AAK76387)
EbdB (β or B-chain) (AAK76388
EbdC (γ or C-chain) (AAK76389)