2E1Z

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A) obtained after co-crystallization with ATP

Summary for 2E1Z

• Entry DOI: 10.2210/pdb2e1z/pdb
• Related: 1X3M 1X3N 2E1Y 2E20
• Descriptor: Propionate Kinase, BIS(ADENOSINE)-5'-TETRAPHOSPHATE, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: propionate kinase, tdcd, native, acetate kinase, nucleotide, ap4a, adp, atp, amppnp, transferase
• Biological source: Salmonella typhimurium
• Total number of polymer chains: 1
• Total formula weight: 46144.85

Authors

Simanshu, D.K.,Savithri, H.S.,Murthy, M.R.N. (deposition date: 2006-11-04, release date: 2007-09-18, Last modification date: 2023-10-25)

Primary citation

Simanshu, D.K.,Savithri, H.S.,Murthy, M.R.N.
Crystal structures of Salmonella typhimurium propionate kinase and its complex with Ap4A: evidence for a novel Ap4A synthetic activity.
Proteins, 70:1379-1388, 2008

PubMed Abstract: Propionate kinase catalyses the last step in the anaerobic breakdown of L-threonine to propionate in which propionyl phosphate and ADP are converted to propionate and ATP. Here we report the structures of propionate kinase (TdcD) in the native form as well as in complex with diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) by X-ray crystallography. Structure of TdcD obtained after cocrystallization with ATP showed Ap4A bound to the active site pocket suggesting the presence of Ap4A synthetic activity in TdcD. Binding of Ap4A to the enzyme was confirmed by the structure determination of a TdcD-Ap4A complex obtained after cocrystallization of TdcD with commercially available Ap4A. Mass spectroscopic studies provided further evidence for the formation of Ap4A by propionate kinase in the presence of ATP. In the TdcD-Ap4A complex structure, Ap4A is present in an extended conformation with one adenosine moiety present in the nucleotide binding site and other in the proposed propionate binding site. These observations tend to support direct in-line transfer of phosphoryl group during the kinase reaction.

PubMed: 17894350
DOI: 10.1002/prot.21626

Experimental method

X-RAY DIFFRACTION (1.98 Å)