Biology subjects

Hashemian, M.

Publications and source records attributed to Hashemian, M..

4 recordsLinked to original sources

bioRxiv2026

Structural Connectivity Between the Zinc Linchpin Motif, the cluster, and the active site orchestrates DNA repair in MUTYH

The DNA glycosylase MUTYH protects genomic integrity by excising adenine mispaired with 8-oxoguanine (OG), which initiates base excision repair (BER). The [4Fe-4S] cluster DNA binding domain and Zn linchpin motif of MUTYH are hotspots for inherited cancer associated variants (CAVs) highlighting their critical functions in DNA repair. Here, we present three full-length human MUTYH crystal structures bound to DNA across three catalytic states, representing early and late transition states and product complexes. These structures reveal a previously unrecognized interplay between the Zn site and the Fe-S cluster mediated by His85 and a conserved Arg247/Arg307 bridge spanning [~]15 [A]. Disruption of this network impairs metal loading, reduces the active enzyme fraction, weakens lesion DNA binding, and diminishes OG:A repair in cells. Moreover, the Zn site adopts distinct coordination modes across the reaction coordinate, with a water molecule replacing a cysteine ligand in transition state analog complexes and cysteine coordination restored in a product-mimicked state. Functional analyses show that this ligand switching is dispensable for core glycosylase chemistry in vitro but disproportionately affects repair in cells, suggesting an additional role of the Zn linchpin in cellular OG:A repair beyond intrinsic glycosylase activity, likely involving interactions with BER partners. Together, these findings illustrate how the Zn linchpin enhances Fe-S cluster domain DNA substrate engagement to enable effective DNA repair and provides a rationale for how these functions are compromised by MUTYH CAVs.

biochemistry↗

bioRxiv2025

Structure, dynamics, and processing of 8oxoG:A in the nucleosome

Eukaryotic genomic DNA is packaged into chromatin through a repeating unit known as the nucleosome. In this chromatin environment, DNA is constantly exposed to several sources of DNA damage, such as reactive oxygen species (ROS), which can lead to the formation of 8-oxo-7,8-dihydroguanine (8oxoG). 8oxoG can base pair with cytosine (8oxoG:C) or form a mutagenic base pair with adenine (8oxoG:A), which can lead to single base transversions if left unrepaired. To date, the structure and dynamics of these two possible 8oxoG base pairs in the nucleosome remain unclear. Furthermore, whether MutY homologue (MUTYH) excises 8oxoG:A base pairs in the nucleosome remains elusive. Here using a combination of cryogenic-electron microscopy, molecular dynamics simulations, and biochemistry we determined the structure and dynamics of 8oxoG:C and 8oxoG:A base pairs in the nucleosome and characterize MUTYH activity in nucleosomal DNA. We found that nucleosomal 8oxoG:C forms a stable base pair using its anti conformation, while nucleosomal 8oxoG:A forms a more dynamic base pair using its syn conformation that is unable to be processed by MUTYH. This work provides fundamental insight into the accommodation of oxidative damage in the nucleosome and how this damage contributes to increased mutagenic transversions in nucleosomal compared to linker DNA.

biochemistry↗

bioRxiv2025

Crystal structure of MutYX: A novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-Oxoguanine recognition sphere

The [4Fe-4S] cluster is an important cofactor of the base excision repair (BER) adenine DNA glycosylase MutY to prevent mutations associated with 8-oxoguanine (OG). Several MutYs lacking the [4Fe-4S] cofactor have been identified. Phylogenetic analysis shows that clusterless MutYs are distributed in two clades suggesting cofactor loss in two independent evolutionary events. Herein, we determined the first crystal structure of a clusterless MutY complexed with DNA. On the basis of the dramatic structural divergence from canonical MutYs, we refer to this as representative of a clusterless MutY subgroup "MutYX". Interestingly, MutYX compensates for the missing [4Fe-4S] cofactor to maintain positioning of catalytic residues by expanding a pre-existing -helix and acquisition of the new -helix. Surprisingly, MutYX also acquired a new C-terminal domain that uniquely recognizes OG using residue Gln201 and Arg209. Adenine glycosylase assays and binding affinity measurements indicate that Arg209 is the primary residue responsible to specificity for OG:A lesions, while Gln201 bridges OG and Arg209. Surprisingly, replacement of Arg209 and Gln201 with Ala increases activity toward G:A mismatches. The MutYX structure serves as an example of devolution, capturing structural features required to retain function in the absence of a metal cofactor considered indispensable.

biochemistry↗

bioRxiv2024

Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its cluster cofactor and active site required for DNA repair

MUTYH is a clinically important DNA glycosylase that thwarts mutations by initiating base-excision repair at 8-oxoguanine (OG):A lesions. The roles for its [4Fe-4S] cofactor in DNA repair remain enigmatic. Functional profiling of cancer-associated variants near the [4Fe-4S] cofactor revealed that most variations abrogate both retention of the cofactor and enzyme activity. Surprisingly, R241Q and N238S retained the metal center and bound substrate DNA tightly but were completely inactive. We solved the crystal structure of human MUTYH bound to a transition state mimic and this revealed that Arg241 and Asn238 build an H-bond network connecting the [4Fe-4S] cluster to the catalytic Asp236 that mediates base excision. The structure of the bacterial MutY variant R149Q, along with molecular dynamics simulations of the human enzyme, show the cofactor functions to position and activate the catalytic Asp. These results suggest that allosteric cross-talk between the DNA binding [4Fe-4S] cofactor and the base excision site regulate DNA repair.

biochemistry↗