5GK2

The structure of the H302A mutant of StlD

Summary for 5GK2

• Entry DOI: 10.2210/pdb5gk2/pdb
• Related: 5GK0 5GK1
• Descriptor: Ketosynthase StlD (2 entities in total)
• Functional Keywords: ketosynthase, transferase
• Biological source: Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
• Total number of polymer chains: 4
• Total formula weight: 178737.50

Authors

Mori, T.,Dngfeng, Y.,Morita, H.,Abe, I. (deposition date: 2016-07-03, release date: 2017-07-05, Last modification date: 2023-11-08)

Primary citation

Mori, T.,Awakawa, T.,Shimomura, K.,Saito, Y.,Yang, D.,Morita, H.,Abe, I.
Structural Insight into the Enzymatic Formation of Bacterial Stilbene.
Cell Chem Biol, 23:1468-1479, 2016

PubMed Abstract: In contrast to stilbene biosynthesis by type III polyketide synthase in plants, in bacteria stilbene is produced by the collaboration of two enzymes in Photorhabdus luminescens: the unusual β-ketosynthase StlD catalyzes the condensation of the β-ketoacyl starter with an α,β-unsaturated-acyl substrate (two C-C bond-forming reactions) to produce isopropylstyrylcyclohexanedione, which is subsequently converted to stilbene by the aromatase StlC. Here we report the in vitro characterizations of StlD and StlC, and the X-ray crystal structures of StlD. Interestingly, structure-based mutagenesis demonstrated that His302, within the conserved Cys-His-Asn triad, is not essential for the enzyme reaction, while Glu154 functions as a base-catalyst to activate the β-ketoacyl intermediate bound to the catalytic Cys126. The structures also revealed the presence of a putative nucleophilic water molecule activated by hydrogen bond networks with Glu154 and Ser340, suggesting that StlD employs novel catalytic machinery for the condensation of two acyl substrates to produce the cyclohexanedione scaffold.

PubMed: 27866911
DOI: 10.1016/j.chembiol.2016.10.010

Experimental method

X-RAY DIFFRACTION (2.201 Å)