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3.D.2 The Proton-translocating Transhydrogenase (PTH) Family

Membrane-associated dimeric proton-translocating, nicotinamide nucleotide transhydrogenases (PTHs; EC catalyze transmembrane translocation of one proton per hydride transferred between NADH and NADP (Jackson et al., 1999; Weston et al., 2002). PTHs are found in some bacteria and in mitochondria from all major groups of eukaryotes. Complete sequences are available from animals, fungi, protozoans and bacteria. Homologues are not present in archaea, in S. cerevisiae and in several bacteria for which complete genomes have been sequenced (Studley et al., 1999). A3-d strcuture is available for a bacterial PTH, and the structures and mechanisms of these proteins have been reviewed (Zhang et al. 2017).

PTH enzymes or enzyme complexes consist of dimers of 1 polypeptide chain (e.g., human PTH), 2 polypeptide chains (e.g., E. coli PTH) or 3 polypeptide chains (e.g., R. rubrum PTH), but all PTH monomers are of about 1000 residues and are homologous throughout their lengths (Hatefi and Yamaguchi, 1996; Yamaguchi and Hatefi, 1994). The animal proteins consist of a hydrophilic N-terminal NAD/NADH-binding domain, a central hydrophobic transmembrane domain of up to 14 transmembrane α-helical spanners, and a C-terminal hydrophilic NADP/NADPH-binding domain. In E. coli, the PTH has been shown to have 13 TMSs, four in the α-subunit and 9 in the β-subunit (Meuller and Rydström, 1999). The C-terminus of the α-subunit and the N-terminus of the β-subunit face the cytosol and periplasm, respectively. The NAD-binding domains are homologous to those of bacterial alanine dehydrogenases and fungal saccharopine dehydrogenases (Studley et al., 1999). The proton-translocation pathway of the PTHs is provided by the central transmembrane domain (Bizouarn et al., 2000, 2002). These enzymes catalyze direct hydride transfer between NAD(H) and NADP(H) in a reaction that is tightly coupled to the transmembrane translocation of a single proton. An imposed proton motive force shifts the equilibrium of the otherwise fully reversible reaction towards NADPH formation (Hatefi and Yamaguchi, 1996; Yamaguchi and Hatefi, 1994). The binding of the 'wrong' nucleotides (NAD+ and NADH instead of NADP+ and NADPH) to the dIII site may lead to slip: proton translocation without change in the nucleotide redox state (Huxley et al., 2011).

3-Dimensional structures of PTH complexed with nucleotide binding components as well as a variety of biochemical and biophysical studies indicate that the dihydronicotinamide ring of NADH can move from a distal position relative to the nicotinamide ring of NADP+ to a proximal position. The movement might be responsible for gating hydride transfer during proton translocation (Cotton et al., 2001; Johansson et al., 2005; Mather et al., 2004; Prasad et al., 1999, 2002; Sedelnikova et al., 2000; Sundaresan et al., 2003; 2005; White et al., 2000). Many mechanistic features are established (Bizouarn et al., 2002; Jackson et al., 2002; Pinheiro et al., 2001; van Boxel et al., 2003). X-ray structural analyses suggest that the two catalytic sites alternate during catalysis. Mutations that inhibit dimerization inhibit NADH binding and greatly lower catalytic activity (Obiozo et al., 2007).

Three invariant amino acids, Arg-127, Asp-135, and Ser-138, in the NAD(H)-binding site of Rhodospirillum rubrum transhydrogenase have been mutated. In each mutant, turnover by the intact enzyme was strongly inhibited. Stopped-flow experiments showed that inhibition results from a block in the steps associated with hydride transfer. Mutation of Asp-135 and Ser-138 had no effect on the binding affinity of either NAD+ or NADH, but mutation of Arg-127 led to much weaker binding of NADH and slightly weaker binding of NAD+. X-ray structures showed that their effects were restricted to the locality of the bound NAD(H). The results were consistent with the suggestion that in the wild-type protein, movement of the Arg-127 side chain, and its hydrogen bonding to Asp-135 and Ser-138, stabilizes the dihydronicotinamide of NADH in the proximal position for hydride transfer (Brondijk et al., 2006; Pedersen et al., 2008).

NADPH/NADP+ homeostasis is critical for countering oxidative stress in cells, and nicotinamide nucleotide transhydrogenase (TH) couples the pmf to the generation of NADPH. Leung et al. 2015 presented the 2.8 Å crystal structure of the transmembrane proton channel domain of TH from Thermus thermophilus (TC# 3.D.2.2.2), and the 6.9 Å crystal structure of the entire enzyme (holo-TH). The membrane domain crystallized as a symmetrical dimer, with each protomer containing a putative proton channel. The holo-TH is a highly asymmetric dimer with the NADPH-binding domain (dIII) in two different orientations. This unusual arrangement suggests a catalytic mechanism in which the two copies of dIII alternatively function in proton translocation and hydride transfer (Leung et al. 2015).

The generalized transport reaction catalyzed by members of the PTH family is:

NADP+ + NADH + H+ (out) NADPH + NAD+ + H+ (in).

References associated with 3.D.2 family:

Bizouarn, T., J. Meuller, M. Axelsson, and J. Rydström. (2000). The transmembrane domain and the proton channel in proton-pumping transhydrogenases. Biochim. Biophys. Acta 1459: 284-290. 11004441
Bizouarn, T., M. Althage, A. Pedersen, A. Tigerstrom, J. Karlsson, C. Johansson, and J. Rydstrom. (2002). The organization of the membrane domain and its interaction with the NADP(H)-binding site in proton-translocating transhydrogenase from E. coli. Biochim. Biophys. Acta 1555: 122-127. 12206903
Brondijk, T.H., G.I. van Boxel, O.C. Mather, P.G. Quirk, S.A. White, and J.B. Jackson. (2006). The role of invariant amino acid residues at the hydride transfer site of proton-translocating transhydrogenase. J. Biol. Chem. 281: 13345-13354. 16533815
Cotton, N.P., S.A. White, S.J. Peake, S. McSweeney, and J.B. Jackson. (2001). The crystal structure of an asymmetric complex of the two nucleotide binding components of proton-translocating transhydrogenase. Structure 9: 165-176. 11250201
Hatefi, Y. and M. Yamaguchi. (1996). Nicotinamide nucleotide transhydrogenase: a model for utilization of substrate binding energy for proton translocation. FASEB J. 10: 444-452. 8647343
Huxley, L., P.G. Quirk, N.P. Cotton, S.A. White, and J.B. Jackson. (2011). The specificity of proton-translocating transhydrogenase for nicotinamide nucleotides. Biochim. Biophys. Acta. 1807: 85-94. 20732298
Jackson, J.B., S.A. White, P.G. Quirk, and J.D. Venning. (2002). The alternating site, binding change mechanism for proton translocation by transhydrogenase. Biochemistry 41: 4173-4185. 11914062
Jackson, J.B., S.J. Peake, and S.A. White. (1999). Structure and mechanism of proton-translocating transhydrogenase. FEBS Lett. 464: 1-8. 10611473
Johansson, T., C. Oswald, A. Pedersen, S. Tornroth, M. Okvist, B.G. Karlsson, J. Rydstrom, and U. Krengel. (2005). X-ray structure of domain I of the proton-pumping membrane protein transhydrogenase from Escherichia coli. J. Mol. Biol. 352: 299-312. 16083909
Kishi, R., M. Imanishi, M. Kobayashi, S. Takenaka, M.T. Madigan, Z.Y. Wang-Otomo, and Y. Kimura. (2020). Quinone transport in the closed light-harvesting 1 reaction center complex from the thermophilic purple bacterium Thermochromatium tepidum. Biochim. Biophys. Acta. Bioenerg 1862: 148307. [Epub: Ahead of Print] 32926863
Leung, J.H., L.A. Schurig-Briccio, M. Yamaguchi, A. Moeller, J.A. Speir, R.B. Gennis, and C.D. Stout. (2015). Structural biology. Division of labor in transhydrogenase by alternating proton translocation and hydride transfer. Science 347: 178-181. 25574024
Mather, O.C., A. Singh, G.I. van Boxel, S.A. White, and J.B. Jackson. (2004). Active-site conformational changes associated with hydride transfer in proton-translocating transhydrogenase. Biochemistry 43: 10952-10964. 15323555
Meuller, J. and J. Rydström. (1999). The membrane topology of proton-pumping Escherichia coli transhydrogenase determined by cysteine labeling. J. Biol. Chem. 274: 19072-19080. 10383409
Obiozo, U.M., T.H. Brondijk, A.J. White, G. van Boxel, T.R. Dafforn, S.A. White, and J.B. Jackson. (2007). Substitution of tyrosine 146 in the dI component of proton-translocating transhydrogenase leads to reversible dissociation of the active dimer into inactive monomers. J. Biol. Chem. 282(50): 36434-36443. 17911104
Padayatti, P.S., J.H. Leung, P. Mahinthichaichan, E. Tajkhorshid, A. Ishchenko, V. Cherezov, S.M. Soltis, J.B. Jackson, C.D. Stout, R.B. Gennis, and Q. Zhang. (2017). Critical Role of Water Molecules in Proton Translocation by the Membrane-Bound Transhydrogenase. Structure. [Epub: Ahead of Print] 28648609
Pedersen, A., G.B. Karlsson, and J. Rydström. (2008). Proton-translocating transhydrogenase: an update of unsolved and controversial issues. J. Bioenerg. Biomembr. 40: 463-473. 18972197
Pinheiro, T.J., J.D. Venning, and J.B. Jackson. (2001). Fast hydride transfer in proton-translocating transhydrogenase revealed in a rapid mixing continuous flow device. J. Biol. Chem. 276: 44757-44761. 11577115
Prasad, G.S., M. Wahlberg, V. Sridhar, V. Sundaresan, M. Yamaguchi, Y. Hatefi, and C.D. Stout. (2002). Crystal structures of transhydrogenase domain I with and without bound NADH. Biochemistry 41: 12745-12754. 12379117
Prasad, G.S., V. Sridhar, M. Yamaguchi, Y. Hatefi, and C.D. Stout. (1999). Crystal structure of transhydrogenase domain III at 1.2 Å resolution. Nat. Struct. Biol. 6: 1126-1131. 10581554
Sedelnikova, S.E., J. Burke, P.A. Buckley, D.W. Rice, J.B. Jackson, N.P. Cotton, R.L. Grimley, and P.J. Baker. (2000). Crystallization of the dI component of transhydrogenase, a proton-translocating membrane protein. Acta Crystallogr. D Biol. Crystallogr. 56: 1170-1172. 10957636
Studley, W.K., M. Yamaguchi, Y. Hatefi, and M.H. Saier, Jr. (1999). Phylogenetic analyses of proton-translocating transhydrogenases. Microbial Comp. Genom. 4: 173-186. 10587945
Sundaresan, V., J. Chartron, M. Yamaguchi, and C.D. Stout. (2005). Conformational diversity in NAD(H) and interacting transhydrogenase nicotinamide nucleotide binding domains. J. Mol. Biol. 346: 617-629. 15670609
Sundaresan, V., M. Yamaguchi, J. Chartron, and C.D. Stout. (2003). Conformational change in the NADP(H) binding domain of transhydrogenase defines four states. Biochemistry 42: 12143-12153. 14567675
van Boxel, G.I., P.G. Quirk, N.P. Cotton, S.A. White, and J.B. Jackson. (2003). Glutamine 132 in the NAD(H)-binding component of proton-translocating transhydrogenase tethers the nucleotides before hydride transfer. Biochemistry 42: 1217-1226. 12564924
Weston, C.J., J.D. Venning, and J.B. Jackson. (2002). The membrane-peripheral subunits of transhydrogenase from Entamoeba histolytica are functional only when dimerized. J. Biol. Chem. 277: 26163-26170. 12004068
White, S.A., S.J. Peake, S. McSweeney, G. Leonard, N.P. Cotton, and J.B. Jackson. (2000). The high-resolution structure of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase from human heart mitochondria. Structure 8: 1-12. 10673423
Yamaguchi, M. and Y. Hatefi. (1994). Energy-transducing nicotinamide nucleotide transhydrogenase: nucleotide sequences of the genes and predicted amino acid sequences of the subunits of the enzyme from Rhodospirillum rubrum. J. Bioeng. Biomembr. 26: 435-445. 7844118
Zhang, Q., P.S. Padayatti, and J.H. Leung. (2017). Proton-Translocating Nicotinamide Nucleotide Transhydrogenase: A Structural Perspective. Front Physiol 8: 1089. 29312000
Zöller, J., S. Hong, M.L. Eisinger, M. Anderson, M. Radloff, K. Desch, R. Gennis, and J.D. Langer. (2022). Ligand binding and conformational dynamics of the nicotinamide nucleotide transhydrogenase revealed by hydrogen/deuterium exchange mass spectrometry. Comput Struct Biotechnol J 20: 5430-5439. 36212541