Download Supplemental results EBI InterPro Scan (version 4.8) protein domain

Supplemental results
EBI InterPro Scan (version 4.8) protein domain analysis of RnfC reveals that S.
fumaroxidans strain MPOB RnfC encodes RnfC beta-barrel sandwich hybrid domain
(IPR026902), NADH:ubiquinone oxidoreductase, 51kDa subunit (IPR010208), alphahelical ferredoxin (IPR009051), C-terminal fumarate reductase (IPR012285), and 4Fe-4S
ferredoxin-type, Fe-S binding domains (IPR017896/017900).
In comparison, the strain UI SynarDRAFT_0709 encodes FAD-binding oxidoreductase
(IPR008333), FAD/NAD(P)-binding oxidoreductase (IPR001433), ferredoxin reductasetype FAD-binding domain (IPR017927), riboflavin synthase-like beta-barrel
(IPR017936), and dihydroorotate dehydrogenase, electron transfer subunit, Fe-S cluster
binding-domain (IPR019480), ferredoxin reductase-like C-terminal domain (SSF52343),
and a transmembrane region. In addition, SynarDRAFT_0710 encodes an alpha-helical
ferredoxin (IPR009051), C-terminal fumarate reductase (IPR012285), and 4Fe-4S
ferredoxin-type, Fe-S binding domains (IPR017896/017900).
The RnfC and SynarDRAFT_0710-0709 clearly share features. In particular, both
possess alphahelical ferredoxin, C-terminal fumarate reductase, 4Fe-4S ferredoxin-type
Fe-S binding domain, and transmembrane beta-barrel domains. Strikingly, both betabarrel domains encode seven beta-strands. Transmembrane beta-barrel are known to act
as selective ion channels (Smythies, 1981; Schulz, 2000; Baumeister et al., 2001;
Delcour, 2002; Menestrina et al., 2003; Som et al., 2003; Moroni and Thiel, 2006; Jang et
al., 2010; Mohammad et al., 2011; Garcia-Gimenez et al., 2012). Given that none of the
other Rnf subunits encode discernable transmembrane ion channels, we speculate that the
RnfC beta-barrel may serve as an ion channel driving reverse electron transport.
Furthermore, the RnfC and SynarDRAFT_0709 beta-barrels may select for ions with
similar size and charge because they are both seven-stranded.
References
Baumeister, B., Sakai, N., and Matile, S. (2001) p-octiphenyl β-barrels with ion channel
and esterase activity. Org Lett 3: 4229-4232.
Delcour, A.H. (2002) Structure and function of pore-forming β-barrels from bacteria. J
Mol Microbiol Biotechnol 4: 1-10.
Garcia-Gimenez, E., Alcaraz, A., and Aguilella, V.M. (2012) Divalent metal ion transport
across large biological ion channels and their effect on conductance and selectivity.
Biochem Res Int 2012: 245786.
Jang, H., Arce, F.T., Ramachandran, S., Capone, R., Lal, R., and Nussinov, R. (2010) βBarrel topology of Alzheimer's beta-amyloid ion channels. J Mol Biol 404: 917-934.
Menestrina, G., Dalla Serra, M., Comai, M., Coraiola, M., Viero, G., Werner, S. et al.
(2003) Ion channels and bacterial infection: the case of β-barrel pore-forming protein
toxins of Staphylococcus aureus. FEBS Lett 552: 54-60.
Mohammad, M.M., Howard, K.R., and Movileanu, L. (2011) Redesign of a plugged βbarrel membrane protein. J Biol Chem 286: 8000-8013.
Moroni, A., and Thiel, G. (2006) Flip-flopping salt bridges gate an ion channel. Nat
Chem Biol 2: 572-573.
Schulz, G.E. (2000) β-Barrel membrane proteins. Curr Opin Struct Biol 10: 443-447.
Smythies, J.R. (1981) On the molecular structure of the ion channel associated with the
acetylcholine receptor: a β-barrel? Med Hypotheses 7: 1095-1098.
Som, A., Sakai, N., and Matile, S. (2003) Complementary characteristics of homologous
p-octiphenyl β-barrels with ion channel and esterase activity. Bioorg Med Chem 11:
1363-1369.