6M72

Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGDP

Summary for 6M72

• Entry DOI: 10.2210/pdb6m72/pdb
• Related: 6M6Y
• Descriptor: Hydrolase, NUDIX family protein, 2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate), PYROPHOSPHATE 2-, ... (5 entities in total)
• Functional Keywords: msmutt1, nudix hydrolase, histidine phosphatase domain, nucleotide pool sanitation enzyme, 8-oxo-dgdp, molecular aggregation, plasticity, enzyme action, hydrolase
• Biological source: Mycolicibacterium smegmatis MC2 155
• Total number of polymer chains: 1
• Total formula weight: 38796.61

Authors

Raj, P.,Karthik, S.,Arif, S.M.,Varshney, U.,Vijayan, M. (deposition date: 2020-03-16, release date: 2020-10-14, Last modification date: 2023-11-29)

Primary citation

Raj, P.,Karthik, S.,Arif, S.M.,Varshney, U.,Vijayan, M.
Plasticity, ligand conformation and enzyme action of Mycobacterium smegmatis MutT1.
Acta Crystallogr D Struct Biol, 76:982-992, 2020

PubMed Abstract: Mycobacterium smegmatis MutT1 (MsMutT1) is a sanitation enzyme made up of an N-terminal Nudix hydrolase domain and a C-terminal domain resembling a histidine phosphatase. It has been established that the action of MutT1 on 8-oxo-dGTP, 8-oxo-GTP and diadenosine polyphosphates is modulated by intermolecular interactions. In order to further explore this and to elucidate the structural basis of its differential action on 8-oxo-NTPs and unsubstituted NTPs, the crystal structures of complexes of MsMutT1 with 8-oxo-dGTP, GMPPNP and GMPPCP have been determined. Replacement soaking was used in order to ensure that the complexes were isomorphous to one another. Analysis of the structural data led to the elucidation of a relationship between the arrangements of molecules observed in the crystals, molecular plasticity and the action of the enzyme on nucleotides. The dominant mode of arrangement involving a head-to-tail sequence predominantly leads to the generation of NDPs. The other mode of packing arrangement appears to preferentially generate NMPs. This work also provides interesting insights into the dependence of enzyme action on the conformation of the ligand. The possibility of modulating the enzyme action through differences in intermolecular interactions and ligand conformations makes MsMutT1 a versatile enzyme.

PubMed: 33021500
DOI: 10.1107/S2059798320010992

Experimental method

X-RAY DIFFRACTION (1.6 Å)