Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters

Arsenate reductase (ArsC) is a superfamily
of enzymes that reduce
arsenate. Due to active site similarities, some ArsC can function
as low-molecular weight protein tyrosine phosphatases (LMW-PTPs).
Broad superfamily classifications align with redox partners (Trx-
or Grx-linked). To understand this superfamily’s mechanistic
diversity, the ArsC superfamily is classified on the basis of active
site features utilizing the tools TuLIP (two-level iterative clustering
process) and autoMISST (automated multilevel iterative sequence searching
technique). This approach identified nine functionally relevant (perhaps
isofunctional) protein groups. Five groups exhibit distinct ArsC mechanisms.
Three are Grx-linked: group 4AA (classical ArsC), group 3AAA (YffB-like),
and group 5BAA. Two are Trx-linked: groups 6AAAAA and 7AAAAAAAA. One
is an Spx-like transcriptional regulatory group, group 5AAA. Three
are potential LMW-PTP groups: groups 7BAAAA, and 7AAAABAA, which have
not been previously identified, and the well-studied LMW-PTP family
group 8AAA. Molecular dynamics simulations were utilized to explore
functional site details. In several families, we confirm and add detail
to literature-based mechanistic information. Mechanistic roles are
hypothesized for conserved active site residues in several families.
In three families, simulations of the unliganded structure sample
specific conformational ensembles, which are proposed to represent
either a more ligand-binding-competent conformation or a pathway toward
a more binding-competent state; these active sites may be designed
to traverse high-energy barriers to the lower-energy conformations
necessary to more readily bind ligands. This more detailed biochemical
understanding of ArsC and ArsC-like PTP mechanisms opens possibilities
for further understanding of arsenate bioremediation and the LMW-PTP
mechanism.