br General Characteristics of the Type
General Characteristics of the Type II Dehydrogenases Alternative NAD(P)H dehydrogenases conduct the reaction of the rotenone-insensitive oxidation of cytosolic and mitochondrial matrix NADH and/or NADPH (Fig. 1) (Melo et al., 2004, Rasmusson et al., 2004, Rasmusson et al., 2008). They catalyze the two-step transfer of electrons to ubiquinone (UQ), providing the bypass of the rotenone-sensitive Complex I (NADH:UQ oxidoreductase, NADH dehydrogenase, or NDH1) when the matrix NAD(P)H is oxidized or the alternative electron path to Complex I when the cytosolic NAD(P)H is oxidized. The NDH2 are small proteins that are tens of kDa (usually 50–60kDa) generally anchored by the C-terminus in the inner mitochondrial membrane and located towards either the matrix (internal dehydrogenases, NDI) or the intermembrane space (external dehydrogenases, NDE) (Melo et al., 2004, Rasmusson et al., 2004, Rasmusson et al., 2008). The manner in which NAD(P)H dehydrogenases are embedded in the membrane remains unclear. There are several reports showing that a hydrophobic environment is necessary for these enzymes to be active (Bandeiras et al., 2003, Bjorklof et al., 2000, Gomes et al., 2001). Some in silico predictions of the secondary structures of type II dehydrogenases revealed putative transmembrane α-helices, e.g., Neurospora crassa NDE1 and Saccharomyces cerevisiae NDI1 (Melo et al. 2004). On the other hand, it has been suggested that the NDH2 interact with the membrane with the aid of amphipathic α-helices, where the hydrophobic and hydrophilic residues are situated on opposite sides on the helical surface (Bandeiras et al., 2002, Melo et al., 2004). In spite of this, the mechanism of the precise tethering of the protein to the membrane is unknown, and further structural studies are necessary to clarify the issue. Type II dehydrogenases are usually monomers or homodimers. Their amino PF-03084014 receptor sequences contain two well conserved motifs to bind nucleotides, one is designated for the noncovalent binding of FAD or FMN, while the second is for NAD(P)H (Kerscher, 2000, Melo et al., 2004, Rasmusson et al., 2004). The NAD(P)H dehydrogenases possess a type I UQ-binding site, whose characteristic feature is one conserved histidine residue flanked downstream by an aliphatic residue (usually leucine) (Fisher and Rich 2000). In addition, the UQ-binding sites differ somewhat between the NDH2 originating from various organisms, probably indicating the adaptation to the UQ molecule present in a particular organism, and thus enabling a more effective protein-UQ interaction (Melo et al. 2004). Alternative NAD(P)H dehydrogenases are classified into three groups depending on the conserved motifs present in their primary sequences and secondary structures. Group A includes the NDH2 with two ADP-binding motifs engaged in the noncovalent binding of NAD(P)H and flavin nucleotides, while group B comprises the NDH2 that possess both ADP-binding motifs and a conserved EF-hand fold that is responsible for calcium binding (Bandeiras et al., 2003, Gomes et al., 2001). The dehydrogenases from both groups are found in eukaryotes, archaea, and bacteria. Group C contains enzymes with a conserved consensus motif in a βαβ fold and with a covalently bound flavin nucleotide. This group has previously been limited to hyperthermophilic archaea, but cyanobacterial proteins and A. thaliana NDC1 and rice NDC homolog have been classified in this group (Michalecka et al. 2003). NDC1 has been found in proteomic analyses in plastoglobules, indicating that it may be present in both mitochondria and chloroplasts (Ytterberg et al. 2006). Thus, the ndc1 gene has been proposed to have entered the plant cell through the chloroplast progenitor and later transferred to the nucleus (Michalecka et al. 2003). NDI and NDE dehydrogenases in plants are correlated to the nda and ndb gene types, respectively (Michalecka et al., 2003, Rasmusson et al., 1999). The plant NDA family is the most similar to a homolog in Trypanosoma brucei. The Neurospora crassa NDE1 contains a conserved segment corresponding to the plant NDB EF-hand domain that is responsible for calcium binding and/or regulation. However, it has been suggested that because of their relatively low level of similarity, these insertions may be descendants of a single evolutionary event, from which the N-terminal EF-hand motif is conserved in the NDB and the C-terminal in the N. crassa NDE1 (Kerscher, 2000, Michalecka et al., 2003). Using molecular modeling, it has been recently demonstrated that the NDB sequences possess different motifs, some of which are the acidic-type, and the others are the non-acidic-type. Among the NDB proteins, the presence of non-acidic and acidic motifs correlates with specificity for NADPH and NADH, respectively (Hao and Rasmusson 2016).