Premium
The three‐dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans ‐aconitate: Insights into its biological function
Author(s) -
Garvey Graeme S.,
Rocco Christopher J.,
EscalanteSemerena Jorge C.,
Rayment Ivan
Publication year - 2007
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.072801907
Subject(s) - shewanella oneidensis , isomerase , aconitase , chemistry , stereochemistry , enzyme , bacteria , dioxygenase , biochemistry , biology , genetics
Abstract In bacteria, the dehydration of 2‐methylcitrate to yield 2‐methylaconitate in the 2‐methylcitric acid cycle is catalyzed by a cofactor‐less (PrpD) enzyme or by an aconitase‐like (AcnD) enzyme. Bacteria that use AcnD also require the function of the PrpF protein, whose function was previously unknown. To gain insights into the function of PrpF, the three‐dimensional crystal structure of the PrpF protein from the bacterium Shewanella oneidensis was solved at 2.0 Å resolution. The protein fold of PrpF is strikingly similar to those of the non‐PLP‐dependent diaminopimelate epimerase from Haemophilus influenzae , a putative proline racemase from Brucella melitensis , and to a recently deposited structure of a hypothetical protein from Pseudomonas aeruginosa . Results from in vitro studies show that PrpF isomerizes trans ‐aconitate to cis ‐aconitate. It is proposed that PrpF catalysis of the cis–trans isomerization proceeds through a base‐catalyzed proton abstraction coupled with a rotation about C2–C3 bond of 2‐methylaconitate, and that residue Lys73 is critical for PrpF function. The newly identified function of PrpF as a non‐PLP‐dependent isomerase, together with the fact that PrpD‐containing bacteria do not require PrpF, suggest that the isomer of 2‐methylaconitate that serves as a substrate of aconitase must have the same stereochemistry as that synthesized by PrpD. From this, it follows that the 2‐methylaconitate isomer generated by AcnD is not a substrate of aconitase, and that PrpF is required to generate the correct isomer. As a consequence, the isomerase activity of PrpF may now be viewed as an integral part of the 2‐methylcitric acid cycle.