4JV3

Crystal structure of beta-ketoacyl synthase from Brucella melitensis in complex with platencin

Summary for 4JV3

• Entry DOI: 10.2210/pdb4jv3/pdb
• Related: 3LRF
• Descriptor: Beta-ketoacyl synthase, 2,4-dihydroxy-3-({3-[(2S,4aS,8S,8aR)-8-methyl-3-methylidene-7-oxo-1,3,4,7,8,8a-hexahydro-2H-2,4a-ethanonaphthalen-8-yl]propanoyl}amino)benzoic acid (3 entities in total)
• Functional Keywords: ssgcid, beta-ketoacyl synthase, platencin, structural genomics, seattle structural genomics center for infectious disease, transferase-antibiotic complex, transferase/antibiotic
• Biological source: Brucella melitensis biovar Abortus
• Total number of polymer chains: 1
• Total formula weight: 46148.81

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID) (deposition date: 2013-03-25, release date: 2013-05-22, Last modification date: 2023-09-20)

Primary citation

Patterson, E.I.,Nanson, J.D.,Abendroth, J.,Bryan, C.,Sankaran, B.,Myler, P.J.,Forwood, J.K.
Structural characterization of beta-ketoacyl ACP synthase I bound to platencin and fragment screening molecules at two substrate binding sites.
Proteins, 88:47-56, 2020

PubMed Abstract: The bacterial fatty acid pathway is essential for membrane synthesis and a range of other metabolic and cellular functions. The β-ketoacyl-ACP synthases carry out the initial elongation reaction of this pathway, utilizing acetyl-CoA as a primer to elongate malonyl-ACP by two carbons, and subsequent elongation of the fatty acyl-ACP substrate by two carbons. Here we describe the structures of the β-ketoacyl-ACP synthase I from Brucella melitensis in complex with platencin, 7-hydroxycoumarin, and (5-thiophen-2-ylisoxazol-3-yl)methanol. The enzyme is a dimer and based on structural and sequence conservation, harbors the same active site configuration as other β-ketoacyl-ACP synthases. The platencin binding site overlaps with the fatty acyl compound supplied by ACP, while 7-hydroxyl-coumarin and (5-thiophen-2-ylisoxazol-3-yl)methanol bind at the secondary fatty acyl binding site. These high-resolution structures, ranging between 1.25 and 1.70 å resolution, provide a basis for in silico inhibitor screening and optimization, and can aid in rational drug design by revealing the high-resolution binding interfaces of molecules at the malonyl-ACP and acyl-ACP active sites.

PubMed: 31237717
DOI: 10.1002/prot.25765

Experimental method

X-RAY DIFFRACTION (1.7 Å)