Repurposing the GNAT Fold in the Initiation of Polyketide Biosynthesis

Meredith A Skiba; Collin L Tran; Qingyun Dan; Andrew P Sikkema; Zachary Klaver; William H Gerwick; David H Sherman; Janet L Smith

doi:10.1016/j.str.2019.11.004

Repurposing the GNAT Fold in the Initiation of Polyketide Biosynthesis

Structure. 2020 Jan 7;28(1):63-74.e4. doi: 10.1016/j.str.2019.11.004. Epub 2019 Nov 27.

Authors

Meredith A Skiba¹, Collin L Tran², Qingyun Dan², Andrew P Sikkema¹, Zachary Klaver², William H Gerwick³, David H Sherman⁴, Janet L Smith⁵

Affiliations

¹ Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
² Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
³ Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.
⁴ Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
⁵ Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA. Electronic address: janetsmith@umich.edu.

Abstract

Natural product biosynthetic pathways are replete with enzymes repurposed for new catalytic functions. In some modular polyketide synthase (PKS) pathways, a GCN5-related N-acetyltransferase (GNAT)-like enzyme with an additional decarboxylation function initiates biosynthesis. Here, we probe two PKS GNAT-like domains for the dual activities of S-acyl transfer from coenzyme A (CoA) to an acyl carrier protein (ACP) and decarboxylation. The GphF and CurA GNAT-like domains selectively decarboxylate substrates that yield the anticipated pathway starter units. The GphF enzyme lacks detectable acyl transfer activity, and a crystal structure with an isobutyryl-CoA product analog reveals a partially occluded acyltransfer acceptor site. Further analysis indicates that the CurA GNAT-like domain also catalyzes only decarboxylation, and the initial acyl transfer is catalyzed by an unidentified enzyme. Thus, PKS GNAT-like domains are re-classified as GNAT-like decarboxylases. Two other decarboxylases, malonyl-CoA decarboxylase and EryM, reside on distant nodes of the superfamily, illustrating the adaptability of the GNAT fold.

Keywords: GCN5-related N-acetyltransferase; biosynthesis; natural products; polyketide synthase.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Acetyltransferases / chemistry*
Acetyltransferases / metabolism*
Crystallography, X-Ray
Humans
Models, Molecular
Polyketides / metabolism*
Protein Domains
Protein Folding
Protein Structure, Secondary

Substances

Polyketides
Acetyltransferases

Abstract

Publication types

MeSH terms

Substances

Grants and funding