2GN2

Crystal structure of tetrameric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium in complex with CMP at 2.5A resolution (Hexagonal form)

Summary for 2GN2

• Entry DOI: 10.2210/pdb2gn2/pdb
• Related: 2GN0 2GN1
• Descriptor: Threonine dehydratase catabolic, SODIUM ION, CYTIDINE-5'-MONOPHOSPHATE, ... (4 entities in total)
• Functional Keywords: tdcb, biodegradative threonine deaminase, plp, cmp, threonine dehydratase, l-threonine metabolism, lyase
• Biological source: Salmonella typhimurium
• Total number of polymer chains: 1
• Total formula weight: 37233.27

Authors

Simanshu, D.K.,Savithri, H.S.,Murthy, M.R.N. (deposition date: 2006-04-09, release date: 2006-11-07, Last modification date: 2023-11-15)

Primary citation

Simanshu, D.K.,Savithri, H.S.,Murthy, M.R.
Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation.
J.Biol.Chem., 281:39630-39641, 2006

PubMed Abstract: Two different pyridoxal 5'-phosphate-containing l-threonine deaminases (EC 4.3.1.19), biosynthetic and biodegradative, which catalyze the deamination of l-threonine to alpha-ketobutyrate, are present in Escherichia coli and Salmonella typhimurium. Biodegradative threonine deaminase (TdcB) catalyzes the first reaction in the anaerobic breakdown of l-threonine to propionate. TdcB, unlike the biosynthetic threonine deaminase, is insensitive to l-isoleucine and is activated by AMP. In the present study, TdcB from S. typhimurium was cloned and overexpressed in E. coli. In the presence of AMP or CMP, the recombinant enzyme was converted to the tetrameric form accompanied by significant enzyme activation. To provide insights into ligand-mediated oligomerization and enzyme activation, crystal structures of S. typhimurium TdcB and its complex with CMP were determined. In the native structure, TdcB is in a dimeric form, whereas in the TdcB.CMP complex, it exists in a tetrameric form with 222 symmetry and appears as a dimer of dimers. Tetrameric TdcB binds to four molecules of CMP, two at each of the dimer interfaces. Comparison of the dimer structure in the ligand (CMP)-free and -bound forms suggests that the changes induced by ligand binding at the dimer interface are essential for tetramerization. The differences observed in the tertiary and quaternary structures of TdcB in the absence and presence of CMP appear to account for enzyme activation and increased binding affinity for l-threonine. Comparison of TdcB with related pyridoxal 5'-phosphate-dependent enzymes points to structural and mechanistic similarities.

PubMed: 17046821
DOI: 10.1074/jbc.M605721200

Experimental method

X-RAY DIFFRACTION (2.5 Å)