6qa2

R80A MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS

spinqualitylabelsall models 6qa2, resolution 2.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6qa2 is a 6 chain structure with sequence from Mycta. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: SO4, TAM Gene: ndk, MRA_2471 (MYCTA) Activity: Nucleoside-diphosphate kinase, with EC number 2.7.4.6 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [NDK_MYCTA] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Publication Abstract from PubMed In order to be fully active and participate in the metabolism of phosphorylated nucleotides, most nucleoside diphosphate kinases (NDPK) have to assemble into stable hexamers. Here we studied the role played by six inter-subunit salt bridges R80-D93 in the stability of NDPK from the pathogen Mycobacterium tuberculosis ( Mt). Mutating R80 into Ala or Asn abolished the salt bridges. Unexpectedly, compensatory stabilizing mechanisms appeared for R80A and R80N mutants and we studied them by biochemical and structural methods. R80A mutant crystallized into I222 space group unusual for NDPK and its hexameric structure revealed occurrence at the trimer interface of a stabilizing hydrophobic patch around the mutation. Functionally relevant, a trimer of the R80A hexamer showed a remodeling of the binding site. In this conformation, the cleft of active site is more open, and then active His117 is more accessible to substrates. HDX-MS analysis of WT, R80A and R80N mutants showed that the remodeled region of the protein is highly solvent accessible indicating that equilibrium between open and closed conformation is possible. We propose that such equilibrium occurs in vivo and explains how bulky substrates access the catalytic His117. Remodeling of the binding site of nucleoside diphosphate kinase revealed by X-Ray structure and H/D exchange.,Dautant A, Henri J, Wales TE, Meyer P, Engen JR, Georgescauld F Biochemistry. 2019 Feb 20. doi: 10.1021/acs.biochem.8b01308. PMID:30785730 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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