Mycobacterium tuberculosis class II apurinic/apyrimidinic‐endonuclease/3′‐5′ exonuclease III exhibits DNA regulated modes of interaction with the sliding DNA β‐clamp |
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| Authors: | Taran Khanam Niyati Rai Ravishankar Ramachandran |
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| Affiliation: | Molecular and Structural Biology Division, CSIR‐Central Drug Research Institute, Lucknow, Uttar Pradesh, India |
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| Abstract: | The class‐II AP‐endonuclease (XthA) acts on abasic sites of damaged DNA in bacterial base excision repair. We identified that the sliding DNA β‐clamp forms in vivo and in vitro complexes with XthA in Mycobacterium tuberculosis. A novel 239QLRFPKK245 motif in the DNA‐binding domain of XthA was found to be important for the interactions. Likewise, the peptide binding‐groove (PBG) and the C‐terminal of β‐clamp located on different domains interact with XthA. The β‐clamp‐XthA complex can be disrupted by clamp binding peptides and also by a specific bacterial clamp inhibitor that binds at the PBG. We also identified that β‐clamp stimulates the activities of XthA primarily by increasing its affinity for the substrate and its processivity. Additionally, loading of the β‐clamp onto DNA is required for activity stimulation. A reduction in XthA activity stimulation was observed in the presence of β‐clamp binding peptides supporting that direct interactions between the proteins are necessary to cause stimulation. Finally, we found that in the absence of DNA, the PBG located on the second domain of the β‐clamp is important for interactions with XthA, while the C‐terminal domain predominantly mediates functional interactions in the substrate's presence. |
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