Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): Insights from kinetic and crystallographic studies
| Autor: | Sanchari Banerjee, H.S. Savithri, Dhirendra K. Simanshu, Mathur R. N. Murthy, Sagar Chittori, Ambika M. V. Murthy, Subashini Mathivanan |
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| Přispěvatelé: | Chittori, Sagar, Simanshu, Dhirendra Kumar, Banerjee, Sanchari, Murthy, Ambika Mosale Venkatesh, Mathivanan, Subashini, Savithri, Handanahal Subbarao, Murthy, Mathur Ramabhadrashastry Narasimha |
| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Salmonella typhimurium
enzyme assay Ethylene Glycol GTP' Stereochemistry Molecular Sequence Data Biophysics Guanosine triphosphate Molecular Dynamics Simulation Molecular Biophysics Unit Crystallography X-Ray short-chain fatty acid metabolism Biochemistry Analytical Chemistry Substrate Specificity chemistry.chemical_compound Bacterial Proteins Nucleotide Magnesium Amino Acid Sequence Molecular Biology x-ray crystallography Enzyme Assays chemistry.chemical_classification Acetate kinase Manganese Alanine Nucleotides Phosphotransferases (Carboxyl Group Acceptor) Ligand (biochemistry) Citric acid cycle Kinetics chemistry protein dynamics Propionate Mutagenesis Site-Directed salmonella typhimurium Propionates Protein Multimerization Adenosine triphosphate Hydrophobic and Hydrophilic Interactions Sequence Alignment |
| Zdroj: | IndraStra Global. |
| ISSN: | 2381-3652 |
| Popis: | Short-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 approximate to butyrate), nucleotides (ATP approximate to GTP > CTP approximate to TTP; dATP > dGTP > dCTP) and metal ions (Mg2+ approximate to Mn2+ > Co2+). 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. (C) 2013 Elsevier B.V. All rights reserved. |
| Databáze: | OpenAIRE |
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