2E1Y: Crystal Structure Of Propionate Kinase (tdcd) From Salmonella Typhimurium

Citation:
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.
PDB ID: 2E1YDownload
MMDB ID: 58681
PDB Deposition Date: 2006/11/4
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.6  Å
Source Organism:
Similar Structures:
Biological Unit for 2E1Y: dimeric; determined by author and by software (PISA)
Molecular Components in 2E1Y
Label Count Molecule
Proteins (2 molecules)
2
Propionate Kinase(Gene symbol: tdcD)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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