The Phosphopantetheinyl Transferases: Catalysis of a Post-Translational Modification Crucial for Life† Cite This: Nat
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NPR REVIEW View Article Online View Journal | View Issue The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life† Cite this: Nat. Prod. Rep.,2014,31,61 Joris Beld,‡a Eva C. Sonnenschein,‡§a Christopher R. Vickery,‡ab Joseph P. Noelb and Michael D. Burkart*a Covering: up to 2013 Although holo-acyl carrier protein synthase, AcpS, a phosphopantetheinyl transferase (PPTase), was characterized in the 1960s, it was not until the publication of the landmark paper by Lambalot et al. in 1996 that PPTases garnered wide-spread attention being classified as a distinct enzyme superfamily. In the past two decades an increasing number of papers have been published on PPTases ranging from Received 11th June 2013 identification, characterization, structure determination, mutagenesis, inhibition, and engineering in DOI: 10.1039/c3np70054b synthetic biology. In this review, we comprehensively discuss all current knowledge on this class of www.rsc.org/npr enzymes that post-translationally install a 40-phosphopantetheine arm on various carrier proteins. 1 Introduction 4.2 The other phosphopantetheinylated proteins and their 2 Types of PPTases PPTases 2.1 Family I: holo-acyl carrier protein synthase (AcpS-type 4.3 Carrier protein recognition by PPTases PPTases) 4.4 Peptide mimics of carrier proteins as substrate of PPTases 2.2 Family II: Sfp-type PPTases 4.5 Regulation by 40-phosphopantetheinylation 2.3 Family III: type I integrated PPTases 5 Structures 3 Importance in primary and secondary metabolism 5.1 Structural features of AcpS-type PPTases Published on 29 November 2013. Downloaded 23/07/2014 00:09:47. 3.1 Bacteria 5.2 Structural features of Sfp-type PPTases 3.2 Archaea 5.3 Structural features of type I integrated PPTases 3.3 Cyanobacteria 5.4 Identication of residues important for PPTase activity 3.4 Protista 5.5 pH and metal effects on PPTase activity 3.5 Fungi 5.6 Activity and specicity for CoA donor 3.6 Type I integrated PPTases 5.7 Measuring the activity of PPTases 3.7 Plants and algae 6 Biotechnological use of PPTases 3.8 Animals 6.1 In vitro labeling 3.9 Homo sapiens 6.2 In vivo tagging and labeling 3.10 Evolution and phylogeny 6.3 Other applications 4 Carrier protein(s) 6.4 Production of natural products in heterologous hosts 4.1 Specicity and activity for carrier proteins 6.5 Drug discovery 7 Outlook 8 Acknowledgements 9 References aDepartment of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA. E-mail: [email protected]; Tel: +1 858 434 1360 1 Introduction bHoward Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Phosphopantetheinyl transferases (PPTases)1 are essential for cell Road, La Jolla, CA 92037, USA viability across all three domains of life: bacteria, archaea and † Electronic supplementary information (ESI) available. See DOI: eukaryota. PPTases post-translationally modify modular and 10.1039/c3np70054b ‡ Authors contributed equally. iterative synthases acting in a processive fashion, namely fatty § Current address: Department of Systems Biology, Technical University of acid synthases (FASs), polyketide synthases (PKSs), and non- Denmark, Søltos Plads 221, 2800 Kgs. Lyngby, Denmark. ribosomal peptide synthetases (NRPSs). The central component of This journal is © The Royal Society of Chemistry 2014 Nat. Prod. Rep.,2014,31,61–108 | 61 View Article Online NPR Review these chain-elongating synthases is non-catalytic and is either a due to chain elongation between the structurally diverse multi- translationally linked domain of a larger polypeptide chain or an enzyme complexes of these pathways. The CP tethers the growing independently translated protein. Regardless, this protein intermediates on a 40-phosphopantetheine (PPant) arm of 20 A˚ component is referred to as a carrier protein (CP), or alternatively through a reactive thioester linkage. PPant is thought of as a as a thiolation domain.2 A CP is responsible for timing and effi- “prosthetic arm” on which all substrates and intermediates of ciency in shuttling the rapidly changing chemical intermediates these pathways are covalently yet transiently held during the orderly progression of enzymatic modications to the extending chain. PPTases mediate the transfer and covalent attachment of Joris Beld received his MSc in PPant arms from coenzyme A (CoA) to conserved serine residues chemical engineering from the of the CP domain through phosphoester bonds. These essential University of Twente, Nether- post-translation protein modications convert inactive apo-syn- lands, under the tutelage of Prof. thases to active holo-synthases (Fig. 1). Recently, mechanistically David Reinhoudt. He obtained distinct classes of enzymes have been identied that require his PhD in biochemistry from the PPant arms for biosynthetic catalysis. These include enzymes ETH Zurich, Switzerland, involved in the biosynthesis of lipid A, D-alanyl-lipoteichoic acid, working on selenium and oxida- tive protein folding in the lab of Prof. Donald Hilvert. He is Joseph Noel obtained a Bachelor currently a postdoctoral fellow at of Science degree in Chemistry UC San Diego involved in a range from the University of Pittsburgh of projects investigating micro- at Johnstown in 1985. He algal and bacterial biochemistry received his Ph.D. in chemistry and fatty acid biosynthesis. from the Ohio State University in 1990, working on the enzymology Eva Sonnenschein graduated of phospholipases with Professor from Kiel University, Germany, in Ming-DawTsai. As a postdoctoral 2007 and received her PhD in fellow with the late Paul B. Sigler Marine Microbiology from Jacobs in the Department of Molecular University Bremen and the Max Biophysics and Biochemistry at Planck Institute for Marine Yale, Joe elucidated the structure Microbiology in 2011. She has of heterotrimeric G-proteins. Joe is currently director of the Jack H. been working as a postdoctoral Skirball Center for Chemical Biology and Proteomics at the Salk researcher at UC San Diego Institute, professor at the Salk Institute and investigator with the Published on 29 November 2013. Downloaded 23/07/2014 00:09:47. exploring the details of secondary Howard Hughes Medical Institute. metabolism in microalgae and aiming towards heterologous expression of natural-product synthases in these organisms. Coming from an aquatic ecology A native Texan, Michael Burkart background, Eva wants to understand the molecular basics of received a BA in chemistry from microbial interactions with the goal to predict community adaption Rice University in 1994. He to environmental changes in the future. received a PhD in Organic Chemistry from the Scripps Christopher Vickery graduated Research Institute in 1999 under from the University of Maryland, the mentorship of Prof. Chi-Huey College Park in 2009 with a B.S. Wong, aer which time he in Biochemistry. He has been a pursued postdoctoral studies at graduate student for Prof. Harvard Medical School with Michael Burkart and Prof. Joseph Prof. Christopher Walsh. Since Noel in the Department of 2002 he has taught and per- Chemistry and Biochemistry at formed research at the University the University of California, San of California, San Diego, where he is a Professor of Chemistry and Diego, and the Salk Institute, Biochemistry and Associate Director of the San Diego Center for since 2009. His current work is Algae Biotechnology. His research interests include natural-product focused on the structural and synthesis and biosynthesis, enzyme mechanism, and metabolic functional characteristics of engineering. Prof. Burkart has been a fellow of the Alfred P. Sloan phosphopantetheinyl transferases and their role in both known and Foundation and Ellison Medical Foundation and was the RSC uncharacterized biosynthetic pathways in different organisms. Organic and Biomolecular Chemistry Lecturer for 2010. 62 | Nat. Prod. Rep.,2014,31,61–108 This journal is © The Royal Society of Chemistry 2014 View Article Online Review NPR (type II). In general, prokaryotes utilize type II FASs and eukaryotes utilize type I FASs. CPs of FASs and PKSs are called acyl carrier proteins (ACPs), whereas the CPs of NRPSs are referred to as peptidyl carrier proteins (PCPs). In order for these synthases to function in primary and secondary metabolism of (iteratively) produced intermediates and products, conserved serine residues of the CPs must be functionalized by PPTase catalysis with a PPant arm. Given the diversity of CP sequences and structures, the PPTase superfamily can be divided into three related yet distinguishable families, based on amino acid sequence conservation and alignments, three-dimensional structures, and their target-elongating synthases. Holo-ACP synthase (AcpS) is the archetypical enzyme of the Fig. 1 General reaction scheme of post-translational phospho- rst family of PPTases recognized (Fig. 2). It encompasses 120 aa, pantetheinylation by a PPTase. The PPTase transfers the PPant moiety forms a homo-trimeric quaternary structure with active sites from CoA to a conserved serine residue on the apo-CP to produce shared across each homotypic interface, and acts on type II FAS holo-CP, here showcased by a typical NRPS module containing the C (condensation), A (adenylation), and CP (carrier protein) domains. 30,50- ACP (AcpP). Surfactin phosphopantetheinyl transferase (Sfp) PAP is 30,50-phosphoadenosine phosphate. represents the second family of PPTases.