8UUC

Crystal structure of a bacterial clusterless MutYX bound to an Abasic site analog (THF) opposite d(8-oxo-G)

Summary for 8UUC

• Entry DOI: 10.2210/pdb8uuc/pdb
• Descriptor: Adenine DNA glycosylase, DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'), DNA (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3'), ... (9 entities in total)
• Functional Keywords: dna glycosylase, base excision repair, dna-protein complex, dna repair, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Eggerthella sp. YY7918; More
• Total number of polymer chains: 3
• Total formula weight: 38229.82

Authors

Trasvina-Arenas, C.H.,David, S.S.,Fisher, A.J. (deposition date: 2023-11-01, release date: 2025-01-22)

Primary citation

Trasvina-Arenas, C.H.,Hashemian, M.,Malek, M.,Merrill, S.,Fisher, A.J.,David, S.S.
Crystal structure of MutYX: A novel clusterless adenine DNA glycosylase with a distinct C-terminal domain and 8-Oxoguanine recognition sphere.
Biorxiv, 2025

PubMed Abstract: 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 α-helix and acquisition of the new α-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.

PubMed: 39803464
DOI: 10.1101/2025.01.03.631205

Experimental method

X-RAY DIFFRACTION (1.55 Å)