8D1U

E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) with an acetylated cysteine and in complex with oxa(dethia)-Coenzyme A

Replaces:  6X7S

Summary for 8D1U

• Entry DOI: 10.2210/pdb8d1u/pdb
• Descriptor: 3-oxoacyl-[acyl-carrier-protein] synthase 3, oxa(dethia)-CoA, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: ketoacyl synthase, substrate analog, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 34577.17

Authors

Benjamin, A.B.,Stunkard, L.M.,Ling, J.,Nice, J.N.,Lohman, J.R. (deposition date: 2022-05-27, release date: 2022-06-15, Last modification date: 2024-10-16)

Primary citation

Benjamin, A.B.,Stunkard, L.M.,Ling, J.,Nice, J.N.,Lohman, J.R.
Structures of chloramphenicol acetyltransferase III and Escherichia coli beta-ketoacylsynthase III co-crystallized with partially hydrolysed acetyl-oxa(dethia)CoA.
Acta Crystallogr.,Sect.F, 79:61-69, 2023

PubMed Abstract: Acetyl coenzyme A (acetyl-CoA) is a reactive metabolite that nonproductively hydrolyzes in a number of enzyme active sites in the crystallization time frame. In order to elucidate the enzyme-acetyl-CoA interactions leading to catalysis, acetyl-CoA substrate analogs are needed. One possible analog for use in structural studies is acetyl-oxa(dethia)CoA (AcOCoA), in which the thioester S atom of CoA is replaced by an O atom. Here, structures of chloramphenicol acetyltransferase III (CATIII) and Escherichia coli ketoacylsynthase III (FabH) from crystals grown in the presence of partially hydrolyzed AcOCoA and the respective nucleophile are presented. Based on the structures, the behavior of AcOCoA differs between the enzymes, with FabH reacting with AcOCoA and CATIII being unreactive. The structure of CATIII reveals insight into the catalytic mechanism, with one active site of the trimer having relatively clear electron density for AcOCoA and chloramphenicol and the other active sites having weaker density for AcOCoA. One FabH structure contains a hydrolyzed AcOCoA product oxa(dethia)CoA (OCoA), while the other FabH structure contains an acyl-enzyme intermediate with OCoA. Together, these structures provide preliminary insight into the use of AcOCoA for enzyme structure-function studies with different nucleophiles.

PubMed: 36862094
DOI: 10.1107/S2053230X23001206

Experimental method

X-RAY DIFFRACTION (1.302 Å)