Isofunctional Clustering and Mechanistic Characterization of the Arsenate Reductase Superfamily Reveals Nine Clusters

Author

Mikaela Rosen, University of Richmond

Date of Award

2020

Document Type

Restricted Thesis: Campus only access

Degree Name

Bachelor of Science

Department

Biology

First Advisor

Dr. Carol Parish

Abstract

Arsenate Reductase (ArsC) is a superfamily of enzymes that reduce arsenate to arsenite. ArsC proteins are vital within arsenic redox microorganisms that lower the concentrations of arsenate and are, therefore, important in the bioremediation strategies that prevent arsenic, a highly toxic and carcinogenic metalloid, from reaching alarming levels in the environment. Previous research suggests different classification and divisions between the arsenate reductases. Three subgroups recognized within the superfamily are the Trx coupled, Grx coupled and Acr2 or eukaryotic ArsC's; these classifications are based on biology and genetics, rather than active site mechanism. The approach described in this contribution is to go beyond the biology and to identify the isofunctional groups, where each group represents a distinct enzyme mechanism represented within this superfamily. The tools applied to this research are the published TuLIP and autoMISST methods, which have been shown to classify proteins based on common features of their functional site. Within the arsenate reductases, nine isofunctional groups were identified: 5 ArsC, 1 transcriptional regulator and 3 low molecular weight protein tyrosine phosphatase (LMW-PTP) groups. This work investigated the potential key residues for each of these isofunctional families. We most thoroughly distinguish two distinct arsenate reductase mechanisms that are Grx coupled: Group 4AA (classical ArsC) a conserved Y-L motif compares structurally to the Group 3AAA (YffB-like) F-H-D motif, and each group has distinct active site motifs of Y-H-N-P-X-C-X2-S-R and Y-G-I-X2-C-X-T-X-K-K, respectively. Additionally, we identify Group 5BAA, another Grx-linked isofunctional family, and two Trx-linked ArsC groups, Groups 6AAAAA and 7AAAAAAAA. We also identify a LMW-PTP group, Group 8AAA, that aligns well with the well-studied LMW-PTP group. Novel protein tyrosine phosphatase (PTP) groups, Groups 7BAAAA, and 7AAAABAA, were also identified; we hypothesize these groups may contain key proteins implicated in many diseases such as cancer, neurodevelopmental disease and diabetes. Molecular dynamics (MD) simulations were utilized to explore these ArsC isofunctional groups and suggest molecular function for conserved residues.

Recommended Citation

Rosen, Mikaela, "Isofunctional Clustering and Mechanistic Characterization of the Arsenate Reductase Superfamily Reveals Nine Clusters" (2020). Honors Theses. 1519.
https://scholarship.richmond.edu/honors-theses/1519