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Microbes & Immunity Identifying hydrogenase orthologs in the human proteome

Given the potential homology between hydrogenases the alignment does reveal conserved homology
and complex I subunit proteins, the active site is particularly immediately preceding the -HPXAHXVLR- motif. The
interesting, as similar sequence alignments could indicate preceding -GPQHP- sequence, positions 85 – 91 (human),
retention of form and function. Notably, the -RGXE- motif contains histidine 88 and two redox-active proline residues
in the catalytic site (Figure 3) is conserved across all (positions 86 and 89), likely close to ubiquinol, which
sequenced proteins, suggesting a distant evolutionary could be key in the partial-to-full reduction of ubiquinone
relationship between NDUFS2 and the large subunits of and downstream immune signaling responses.
[NiFe] hydrogenases. The conserved glutamic acid residue Further along the sequence, at positions 228 – 232, there
(glutamic acid 119 in NDUFS2) may be pertinent to proton is another conserved motif, -RPGGV-. Although it has
transfer. 65 not yet been identified as a site for protein modification,
While this study identified limited homology between its conservation throughout the examined hydrogenases
the aligned regions of NDUFS2 and microbial hydrogenase suggests that it may play a critical role in protein structure
active sites, the redox-sensitive tyrosine 151 residue may and function. Although speculative, the idea that NDUFS2
be involved in the electron transfer chain, conserved only serves as a key oxygen-sensing module and a regulator of
in Ca. Heimdallarchaeota. This is significant, as a crystal complex I activity suggests that these residues may be
73
structure analysis of NDUFS2, conducted by Kampjut and relevant as sites of H activity. H could protect these sites
2
2
Sazanov, 68,69 demonstrated that the ubiquinone molecule from autoxidation, thereby facilitating optimal protein
docks within 4.5 Å of tyrosine 108 in the ovine NDUFS2 function.
module, corresponding to the human equivalent, tyrosine The structural relationship between the proton-
151. In NDUFS2, the redox-sensitive tyrosine 151 residue transferring NDUFS2 and the FeS (N2)-containing
may be involved in redox-regulated reactions central to NDUFS7 subunit indicates that this specific region of the
the complex’s function. Given that tyrosine 95 in MbhL ubiquinone binding module is likely responsible for electron
is also conserved (Figure 2), this could indicate a similar transfer. By reducing electron leakage and subsequent ROS
role in electron transport within Ca. Heimdallarchaeota. formation through structural maintenance, H could have
Furthermore, tyrosine residues often contribute to significant downstream cellular effects. For example, the
2
protein stability through hydrophobic interactions and H 2 protein kinase C (PKC) phosphorylation site (-RASPRQS-)
bonding. 70,71 Therefore, preventing the oxidation of these in the smaller subunit shares the most sequence identity
conserved tyrosines may be critical for H in maintaining among species (Figure 4). If H modulates phosphorylation
2
2
the protein’s structural integrity, especially in regions vital in this region, it could influence the cellular signaling
for its function. cascades that regulate the expression of proinflammatory
The structural analysis of NDUFS2 further identifies factors such as NFκB and TNF-α in mammalian
histidine 59 and asparagine 160 (in ovine), corresponding physiology. Interestingly, H is noted to influence other
2
to histidine 112 and asparagine 182 (in humans), as protein kinase pathways, including MAPK. 20,21 Therefore,
potential candidates for proton translocation. It has been this raises the question of whether H could influence the
69
2
proposed that a proton shuttling mechanism among this activity of this relatively well-conserved region, which is
triad of residues (asparagine, histidine, and tyrosine) could likely crucial for understanding H bioactivity in humans.
2
create a negative charge, enhancing ubiquinone binding Recent investigations utilizing a combination of mass
potential and lowering the redox potential of the N2 FeS spectroscopy and in silico modeling of the NDUFS7 unit
cluster, thereby facilitating electron transfer. Therefore, identified that bovine arginines 108 and 112 (arginine
69
although the catalytic ability may have been lost through 111 and 115 in humans) within the highly conserved
evolution, H could still influence complex 1 dynamics C-terminal -RASPRQ- motif were integral for retaining
2
through interactions with redox-sensitive residues. ubiquinone in the hydrophobic cavity. Nevertheless, it
74
Wirth et al. further suggest that redox functionality remains unclear whether direct electron transfer activity
72
likely exists within the β1–β2 helices of NDUFS2 at positions occurs at either of these moieties. If H stabilizes this region
2
88 – 96 (human), showing the -HPXAHXVLR- arrangement or prevents oxidative damage, it is likely that a steady
(Figure 3). Histidine 88 and histidine 92 of this sequence supply of electrons would be available for the complete
are situated in close proximity to both ubiquinol and reduction of ubiquinone to ubiquinol, thereby enhancing
the terminal 4Fe-4S cluster (N2) of NDUFS7, which the immediate antioxidant potential of the mitochondria.
may provide the redox sensitivity required for electron This could have significant downstream effects, including
transfer to ubiquinone. However, this region is not an increased membrane potential and reduced cellular
well conserved across the species studied. Nonetheless, stress response. 75,76

Volume 1 Issue 2 (2024) 87 doi: 10.36922/mi.4544