2GN0
Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 1.7 A resolution (Triclinic form with one complete subunit built in alternate conformation)
Summary for 2GN0
| Entry DOI | 10.2210/pdb2gn0/pdb |
| Related | 2GN1 2GN2 |
| Descriptor | Threonine dehydratase catabolic, SODIUM ION (3 entities in total) |
| Functional Keywords | tdcb, biodegradative threonine deaminase, plp, threonine dehydratase, l-threonine metabolism, alternate conformation, lyase |
| Biological source | Salmonella typhimurium |
| Total number of polymer chains | 4 |
| Total formula weight | 147594.32 |
| Authors | Simanshu, D.K.,Savithri, H.S.,Murthy, M.R. (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 Cited by 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: 17046821DOI: 10.1074/jbc.M605721200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
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