4WX9

Crystal structure of Mycobacterium tuberculosis OGT in complex with DNA

Summary for 4WX9

• Entry DOI: 10.2210/pdb4wx9/pdb
• Descriptor: DNA (5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3'), DNA (5'-D(P*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3'), Methylated-DNA--protein-cysteine methyltransferase, ... (5 entities in total)
• Functional Keywords: direct dna damage reversal, alkylated dna-protein alkyltransferase, protein-dna complex, transferase
• Biological source: Mycobacterium tuberculosis; More
• Cellular location: Cytoplasm : P9WJW5
• Total number of polymer chains: 5
• Total formula weight: 61656.80

Authors

Miggiano, R.,Rossi, F.,Garavaglia, S.,Rizzi, M. (deposition date: 2014-11-13, release date: 2015-11-04, Last modification date: 2024-01-10)

Primary citation

Miggiano, R.,Perugino, G.,Ciaramella, M.,Serpe, M.,Rejman, D.,Pav, O.,Pohl, R.,Garavaglia, S.,Lahiri, S.,Rizzi, M.,Rossi, F.
Crystal structure of Mycobacterium tuberculosis O6-methylguanine-DNA methyltransferase protein clusters assembled on to damaged DNA.
Biochem.J., 473:123-133, 2016

PubMed Abstract: Mycobacterium tuberculosis O(6)-methylguanine-DNA methyltransferase (MtOGT) contributes to protect the bacterial GC-rich genome against the pro-mutagenic potential of O(6)-methylated guanine in DNA. Several strains of M. tuberculosis found worldwide encode a point-mutated O(6)-methylguanine-DNA methyltransferase (OGT) variant (MtOGT-R37L), which displays an arginine-to-leucine substitution at position 37 of the poorly functionally characterized N-terminal domain of the protein. Although the impact of this mutation on the MtOGT activity has not yet been proved in vivo, we previously demonstrated that a recombinant MtOGT-R37L variant performs a suboptimal alkylated-DNA repair in vitro, suggesting a direct role for the Arg(37)-bearing region in catalysis. The crystal structure of MtOGT complexed with modified DNA solved in the present study reveals details of the protein-protein and protein-DNA interactions occurring during alkylated-DNA binding, and the protein capability also to host unmodified bases inside the active site, in a fully extrahelical conformation. Our data provide the first experimental picture at the atomic level of a possible mode of assembling three adjacent MtOGT monomers on the same monoalkylated dsDNA molecule, and disclose the conformational flexibility of discrete regions of MtOGT, including the Arg(37)-bearing random coil. This peculiar structural plasticity of MtOGT could be instrumental to proper protein clustering at damaged DNA sites, as well as to protein-DNA complexes disassembling on repair.

PubMed: 26512127
DOI: 10.1042/BJ20150833

Experimental method

X-RAY DIFFRACTION (3 Å)