5K87

crystal structure of malonate bound to methylaconitate isomerase PrpF from Shewanella oneidensis

Summary for 5K87

• Entry DOI: 10.2210/pdb5k87/pdb
• Descriptor: 2-methyl-aconitate isomerase, MALONATE ION (3 entities in total)
• Functional Keywords: prpf methylaconitate isomerase 2-mmc, isomerase
• Biological source: Shewanella oneidensis
• Total number of polymer chains: 2
• Total formula weight: 83980.88

Authors

Rayment, I.,Wetterhorn, K. (deposition date: 2016-05-27, release date: 2017-05-31, Last modification date: 2023-09-27)

Primary citation

Rocco, C.J.,Wetterhorn, K.M.,Garvey, G.S.,Rayment, I.,Escalante-Semerena, J.C.
The PrpF protein of Shewanella oneidensis MR-1 catalyzes the isomerization of 2-methyl-cis-aconitate during the catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle.
PLoS ONE, 12:e0188130-e0188130, 2017

PubMed Abstract: The 2-methylcitric acid cycle (2-MCC) is a common route of propionate catabolism in microorganisms. In Salmonella enterica, the prpBCDE operon encodes most of the 2-MCC enzymes. In other organisms, e.g., Shewanella oneidensis MR-1, two genes, acnD and prpF replace prpD, which encodes 2-methylcitrate dehydratase. We showed that together, S. oneidensis AcnD and PrpF (SoAcnD, SoPrpF) compensated for the absence of PrpD in a S. enterica prpD strain. We also showed that SoAcnD had 2-methylcitrate dehydratase activity and that PrpF has aconitate isomerase activity. Here we report in vitro evidence that the product of the SoAcnD reaction is an isomer of 2-methyl-cis-aconitate (2-MCA], the product of the SePrpD reaction. We show that the SoPrpF protein isomerizes the product of the AcnD reaction into the PrpD product (2-MCA], a known substrate of the housekeeping aconitase (AcnB]. Given that SoPrpF is an isomerase, that SoAcnD is a dehydratase, and the results from in vivo and in vitro experiments reported here, it is likely that 4-methylaconitate is the product of the AcnD enzyme. Results from in vivo studies using a S. enterica prpD strain show that SoPrpF variants with substitutions of residues K73 or C107 failed to support growth with propionate as the sole source of carbon and energy. High-resolution (1.22 Å) three-dimensional crystal structures of PrpFK73E in complex with trans-aconitate or malonate provide insights into the mechanism of catalysis of the wild-type protein.

PubMed: 29145506
DOI: 10.1371/journal.pone.0188130

Experimental method

X-RAY DIFFRACTION (1.219 Å)