4fwp | pdb_00004fwp
Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with GDP
Structural highlights
Function[TDCD_SALTY] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881] Publication Abstract from PubMedShort-chain fatty acids (SCFAs) play a major role in carbon cycle and can be utilized as a source of carbon and energy by bacteria. Salmonella typhimurium propionate kinase (StTdcD) catalyzes reversible transfer of the gamma-phosphate of ATP to propionate during l-threonine degradation to propionate. Kinetic analysis revealed that StTdcD possesses broad ligand specificity and could be activated by various SCFAs (propionate>acetate approximately butyrate), nucleotides (ATP approximately GTP>CTP approximately TTP; dATP>dGTP>dCTP) and metal ions (Mg(2+) approximately Mn(2+)>Co(2+)). Inhibition of StTdcD by tricarboxylic acid (TCA) cycle intermediates such as citrate, succinate, alpha-ketoglutarate and malate suggests that the enzyme could be under plausible feedback regulation. Crystal structures of StTdcD bound to PO4 (phosphate), AMP, ATP, Ap4 (adenosine tetraphosphate), GMP, GDP, GTP, CMP and CTP revealed that binding of nucleotide mainly involves hydrophobic interactions with the base moiety and could account for the broad biochemical specificity observed between the enzyme and nucleotides. Modeling and site-directed mutagenesis studies suggest Ala88 to be an important residue involved in determining the rate of catalysis with SCFA substrates. Molecular dynamics simulations on monomeric and dimeric forms of StTdcD revealed plausible open and closed states, and also suggested role for dimerization in stabilizing segment 235-290 involved in interfacial interactions and ligand binding. Observation of an ethylene glycol molecule bound sufficiently close to the gamma-phosphate in StTdcD complexes with triphosphate nucleotides supports direct in-line phosphoryl transfer. Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies.,Chittori S, Simanshu DK, Banerjee S, Murthy AM, Mathivanan S, Savithri HS, Murthy MR Biochim Biophys Acta. 2013 Oct;1834(10):2036-44. doi:, 10.1016/j.bbapap.2013.05.020. Epub 2013 Jun 5. PMID:23747922[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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