4BKQ

Enoyl-ACP reductase from Yersinia pestis (wildtype)with cofactor NADH

Summary for 4BKQ

• Entry DOI: 10.2210/pdb4bkq/pdb
• Related: 4BKO 4BKR 4BKU
• Descriptor: PUTATIVE REDUCTASE YPZ3_3519, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE (3 entities in total)
• Functional Keywords: oxidoreductase, fatty acid biosynthesis
• Biological source: YERSINIA PESTIS
• Total number of polymer chains: 1
• Total formula weight: 46601.17

Authors

Hirschbeck, M.W.,Neckles, C.,Tonge, P.J.,Kisker, C. (deposition date: 2013-04-29, release date: 2014-05-14, Last modification date: 2023-12-20)

Primary citation

Neckles, C.,Pschibul, A.,Lai, C.,Hirschbeck, M.,Kuper, J.,Davoodi, S.,Zou, J.,Liu, N.,Pan, P.,Shah, S.,Daryaee, F.,Bommineni, G.R.,Lai, C.,Simmerling, C.,Kisker, C.,Tonge, P.J.
Selectivity of Pyridone- and Diphenyl Ether-Based Inhibitors for the Yersinia Pestis Fabv Enoyl-Acp Reductase.
Biochemistry, 55:2992-, 2016

PubMed Abstract: The enoyl-ACP reductase (ENR) catalyzes the last reaction in the elongation cycle of the bacterial type II fatty acid biosynthesis (FAS-II) pathway. While the FabI ENR is a well-validated drug target in organisms such as Mycobacterium tuberculosis and Staphylococcus aureus, alternate ENR isoforms have been discovered in other pathogens, including the FabV enzyme that is the sole ENR in Yersinia pestis (ypFabV). Previously, we showed that the prototypical ENR inhibitor triclosan was a poor inhibitor of ypFabV and that inhibitors based on the 2-pyridone scaffold were more potent [Hirschbeck, M. (2012) Structure 20 (1), 89-100]. These studies were performed with the T276S FabV variant. In the work presented here, we describe a detailed examination of the mechanism and inhibition of wild-type ypFabV and the T276S variant. The T276S mutation significantly reduces the affinity of diphenyl ether inhibitors for ypFabV (20-fold → 100-fold). In addition, while T276S ypFabV generally displays an affinity for 2-pyridone inhibitors higher than that of the wild-type enzyme, the 4-pyridone scaffold yields compounds with similar affinity for both wild-type and T276S ypFabV. T276 is located at the N-terminus of the helical substrate-binding loop, and structural studies coupled with site-directed mutagenesis reveal that alterations in this residue modulate the size of the active site portal. Subsequently, we were able to probe the mechanism of time-dependent inhibition in this enzyme family by extending the inhibition studies to include P142W ypFabV, a mutation that results in a gain of slow-onset inhibition for the 4-pyridone PT156.

PubMed: 27136302
DOI: 10.1021/ACS.BIOCHEM.5B01301

Experimental method

X-RAY DIFFRACTION (2.3 Å)