Figure legends
Figure 1 . DsrAB phylogenetic reconstruction showing the
taxonomic affiliation of Dsr-hosting organisms and their environmen-tal
origin. The Maximum Likelihood reconstruction was conducted on a
concatenated alignment of DsrA and DsrB subunits from a curated database
comprising the previously recognized primary homolog groups. The scale
bar shows the expected substitutions per site. The environmental origin
of Dsr homologs is shown based on available metadata associated with the
previously published data-base (Muller et al. 2015) or from metadata
associated with MAGs from metagenomes. Taxonomic classification is given
based on information in the aforementioned database or by
>80% amino acid homology to Dsr from cultivars/genomes
with taxonomic annotation.
Figure 2. Available Crystal Structures of Dsr and a Homology
Model of an Early Evolving Dsr From a Sulfite Reducing Euryarchaeote
(MV2). A-C) side view; D-F) top view; A and D) Archaeoglobus.
fulgidus heterotetramer – pdb id: 3mmc, B and E) Desulfovibrio.
vulgaris hetero-hexamer - pdb id: 2v4j, C and F) homology model of
MV2-Eury hetero-hexamer. Chain colors are: A1 (green), B1 (cyan), A2
(light pink), B2 (light blue), C1 and C2 where present (purple and
white, respectively). Sirohemes (red), siro-hydrochlorine (salmon), and
Fe-S centers (yellow) are sticks or spheres. The sulfite substrate is
shown in the D. vulgaris structure (B) in dark blue spheres.
Figure 3 . Close-up view of the “lower” prosthetic group in
the structure of Dsr. A) A. fulgidus and B) D. vulgaris Chain colors are
: A1 (green), B1 (cyan), Sirohemes (red), siro-hydrochlorine (salmon)
and Fe-S centers (yellow) are sticks or spheres. Trp 119 and Thr 135 are
shown in spheres and colored by element.
Figure 4 . AlphaFold2 model of MV2.Eury DsrAB. The sequence is
colored for pLDDT score (descried in the text), with dark blue
corresponding to high confidence prediction (96%) and red to low
confidence prediction (43%).The view is a top view of the structure as
in Figure 1F. The light blue to red region on the center left and right
correspond to residues 50-62 if the A subunit which interact with the
DsrC electron donating subunit (Figure 1E, F). The upper left, bottom
right and center red regions are the chain termini.
Figure 5 . The heme road FPEC residues in the structure of DsrAB
from A. fulgidus . A) Side view B) top view, C) slab of a zoom
from the top view Distances between FPEC residues are shown in yellow.
Chain colors are: A1 (green), B1 (cyan), A2 (light pink), B2 (light
blue). Sirohemes (red sticks) and Fe-S centers (yellow) are also shown.
Heme road FPEC residues (blue spheres) tracing a connection between
functional hemes are from left to right N180B1, N393A2, T351B1, T351B2,
N393A1 and N180B2. N222A1/2 (also blue spheres) interacts with the
propionate group of the structural (non-functional) heme visible in (A)
in a lower plane. D) Network of aromatic residues connect-ing the
residues of the heme road (dark blue) for the left half of the heme
road. Three aromatic residues, F317A1, F394A2 and Y348B1, directly
connect the heme road residues. These interactions are stabilized from
above by N246B1. N246B1 also contacts C244B1 that makes contact with the
second Fe-S center distal to the siroheme. Two heme road residues T351B2
and N393A1 of the second heterodimer also appear on the right of the
figure.
Figure 6 . Comparison of the heme road FPEC residues in DsrAB.
A). D. vulgaris B), the homology model of MV2-Eury. Slab of a
zoom from the top views. Chain colors are: A1 (green), B1 (cyan), A2
(light pink), B2 (light blue). Sirohemes (red sticks) and Fe-S centers
(yellow) are also shown. FPEC residues (blue spheres) tracing a
connection between functional hemes in the D. vulgaris structure (A) are
from left to right N191B1 (blue spheres), N410A2 (blue spheres), P368B1
(CPK spheres), P368B2 (CPK spheres), N410A1 (blue spheres) and N191B2
(blue spheres) make up the heme road. The corresponding residues in the
MV2.Eury model (B) are from left to right S167B1 (blue spheres), N369A2
(blue spheres), R337B1 (CPK spheres), R337B2 (CPK spheres), N369A1 (blue
spheres) and S167B2 (blue spheres). Note that the sulfite ion is shown
in darer blue bound to the heme in the D. vulgaris structure (A).
Figure 7 . Internal water molecules in the A1B1 heterodimer of
the A. fulgidus structure of DsrAB (A) Full heterodimer and (B)
Zoom in the siroheme. Chain colors are: A1 (green), B1 (cyan). Sirohemes
(red sticks) and Fe-S centers (yellow) are also shown. Internal water
molecules are shown as red spheres. The tryptophan residue blocking
access to the structural (lower) heme is shown in CPK spheres.
Figure 8 . Zoom view of the overlaid structures of DsrAB fromA. fulgidus (cyan), D. vulgaris (dark cyan, and MV2 Eury
(pale cyan. The DsrB subunit insert in the A. fulgidus structure is in
light pink, while the bacterial B loop is magenta. The DsrA subunit
insert in the D. vulgaris structure is wheat. The rest of the DsrA1
subunits are green. Some of the FPEC residues (K and F/D/F) are
indicated in red stick and distances between them (7.4 and 26.7 Å are
indicated). The lysine residues of the FPEC form a salt bridge with a
glutamate from the DsrA subunit (2.7 Å).
Figure 9 . DsrAB phylogenetic reconstruction showing the
taxonomic affiliation of Dsr-hosting organisms and the presence of DsrA
and DsrB structural inserts. The Maximum Likelihood reconstruction was
conducted on a concatenated alignment of DsrA and DsrB subunits from a
curated database comprising the previously recognized primary homolog
groups. Scale bar shows the expected substitutions per site. Taxonomic
classification is given based on information in the database (Muller et
al. 2015) or by >80% amino acid homology to Dsr from
cultivars/genomes with taxonomic annotation. DsrA or DsrB inserts were
identified based on structural characterizations and subsequent
identification within DsrA or DsrB alignments.