1
|
Chen A, Re RN, Davis TD, Tran K, Moriuchi YW, Wu S, La Clair JJ, Louie GV, Bowman ME, Clarke DJ, Mackay CL, Campopiano DJ, Noel JP, Burkart MD. Visualizing the Interface of Biotin and Fatty Acid Biosynthesis through SuFEx Probes. J Am Chem Soc 2024; 146:1388-1395. [PMID: 38176024 DOI: 10.1021/jacs.3c10181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Site-specific covalent conjugation offers a powerful tool to identify and understand protein-protein interactions. In this study, we discover that sulfur fluoride exchange (SuFEx) warheads effectively crosslink the Escherichia coli acyl carrier protein (AcpP) with its partner BioF, a key pyridoxal 5'-phosphate (PLP)-dependent enzyme in the early steps of biotin biosynthesis by targeting a tyrosine residue proximal to the active site. We identify the site of crosslink by MS/MS analysis of the peptide originating from both partners. We further evaluate the BioF-AcpP interface through protein crystallography and mutational studies. Among the AcpP-interacting BioF surface residues, three critical arginine residues appear to be involved in AcpP recognition so that pimeloyl-AcpP can serve as the acyl donor for PLP-mediated catalysis. These findings validate an evolutionary gain-of-function for BioF, allowing the organism to build biotin directly from fatty acid biosynthesis through surface modifications selective for salt bridge formation with acidic AcpP residues.
Collapse
Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Rebecca N Re
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Tony D Davis
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Kelley Tran
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Yuta W Moriuchi
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Sitong Wu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| | - Gordon V Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - David J Clarke
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - C Logan Mackay
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - Dominic J Campopiano
- EaSTCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Rd, Edinburgh EH9 3FJ, U.K
| | - Joseph P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, San Diego, California 92037, United States
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, San Diego, California 92093, United States
| |
Collapse
|
2
|
Jiang Z, Chen A, Chen J, Sekhon A, Louie GV, Noel JP, La Clair JJ, Burkart MD. Masked cerulenin enables a dual-site selective protein crosslink. Chem Sci 2023; 14:10925-10933. [PMID: 37829009 PMCID: PMC10566503 DOI: 10.1039/d3sc02864j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/02/2023] [Indexed: 10/14/2023] Open
Abstract
Protein-reactive natural products such as the fungal metabolite cerulenin are recognized for their value as therapeutic candidates, due to their ability to selectively react with catalytic residues within a protein active site or a complex of protein domains. Here, we explore the development of fatty-acid and polyketide-synthase probes by synthetically modulating cerulenin's functional moieties. Using a mechanism-based approach, we reveal unique reactivity within cerulenin and adapt it for fluorescent labeling and crosslinking of fatty-acid and iterative type-I polyketide synthases. We also describe two new classes of silylcyanohydrin and silylhemiaminal masked crosslinking probes that serve as new tools for activity and structure studies of these biosynthetic pathways.
Collapse
Affiliation(s)
- Ziran Jiang
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Jeffrey Chen
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Arman Sekhon
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Gordon V Louie
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics La Jolla CA 92037 USA
| | - Joseph P Noel
- The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics La Jolla CA 92037 USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093-0358 USA
| |
Collapse
|
3
|
Dietl A, Wellach K, Mahadevan P, Mertes N, Winter S, Kutsch T, Walz C, Schlichting I, Fabritz S, Barends TM. Structures of an unusual 3-hydroxyacyl dehydratase (FabZ) from a ladderane-producing organism with an unexpected substrate preference. J Biol Chem 2023; 299:104602. [PMID: 36907440 PMCID: PMC10139942 DOI: 10.1016/j.jbc.2023.104602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
The genomes of anaerobic ammonium-oxidizing (anammox) bacteria contain a gene cluster comprising genes of unusual fatty acid biosynthesis enzymes that were suggested to be involved in the synthesis of the unique "ladderane" lipids produced by these organisms. This cluster encodes an acyl carrier protein (denoted as "amxACP") and a variant of FabZ, an ACP-3-hydroxyacyl dehydratase. In this study, we characterize this enzyme, which we call anammox-specific FabZ ("amxFabZ"), to investigate the unresolved biosynthetic pathway of ladderane lipids. We find that amxFabZ displays distinct sequence differences to "canonical" FabZ, such as a bulky, apolar residue on the inside of the substrate binding tunnel, where the canonical enzyme has a glycine. Additionally, substrate screens suggest that amxFabZ efficiently converts substrates with acyl chain lengths of up to eight carbons, whereas longer substrates are converted much more slowly under the conditions used. We also present crystal structures of amxFabZs, mutational studies and the structure of a complex between amxFabZ and amxACP, which show that the structures alone cannot explain the apparent differences from canonical FabZ. Moreover, we find that while amxFabZ does dehydrate substrates bound to amxACP, it does not convert substrates bound to canonical ACP of the same anammox organism. We discuss the possible functional relevance of these observations in the light of proposals for the mechanism for ladderane biosynthesis.
Collapse
Affiliation(s)
- Andreas Dietl
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany.
| | - Kathrin Wellach
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Pavithra Mahadevan
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Nicole Mertes
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - SophieL Winter
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Tobias Kutsch
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Carlo Walz
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Ilme Schlichting
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Sebastian Fabritz
- Mass Spectrometry Core Facility, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - ThomasR M Barends
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, D-69120 Heidelberg, Germany.
| |
Collapse
|
4
|
Chen A, Mindrebo JT, Davis TD, Kim WE, Katsuyama Y, Jiang Z, Ohnishi Y, Noel JP, Burkart MD. Mechanism-based cross-linking probes capture the Escherichia coli ketosynthase FabB in conformationally distinct catalytic states. Acta Crystallogr D Struct Biol 2022; 78:1171-1179. [PMID: 36048156 PMCID: PMC9435599 DOI: 10.1107/s2059798322007434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/20/2022] [Indexed: 11/10/2022] Open
Abstract
Ketosynthases (KSs) catalyse essential carbon-carbon bond-forming reactions in fatty-acid biosynthesis using a two-step, ping-pong reaction mechanism. In Escherichia coli, there are two homodimeric elongating KSs, FabB and FabF, which possess overlapping substrate selectivity. However, FabB is essential for the biosynthesis of the unsaturated fatty acids (UFAs) required for cell survival in the absence of exogenous UFAs. Additionally, FabB has reduced activity towards substrates longer than 12 C atoms, whereas FabF efficiently catalyses the elongation of saturated C14 and unsaturated C16:1 acyl-acyl carrier protein (ACP) complexes. In this study, two cross-linked crystal structures of FabB in complex with ACPs functionalized with long-chain fatty-acid cross-linking probes that approximate catalytic steps were solved. Both homodimeric structures possess asymmetric substrate-binding pockets suggestive of cooperative relationships between the two FabB monomers when engaged with C14 and C16 acyl chains. In addition, these structures capture an unusual rotamer of the active-site gating residue, Phe392, which is potentially representative of the catalytic state prior to substrate release. These structures demonstrate the utility of mechanism-based cross-linking methods to capture and elucidate conformational transitions accompanying KS-mediated catalysis at near-atomic resolution.
Collapse
Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Jeffrey T. Mindrebo
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Tony D. Davis
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Woojoo E. Kim
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yohei Katsuyama
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ziran Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Yasuo Ohnishi
- Department of Biotechnology, The Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Joseph P. Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| |
Collapse
|