Crystal structure of the putative cyclase IdmH from the indanomycin nonribosomal peptide synthase/polyketide synthase

Drulyte, Ieva; Obajdin, Jana; Trinh, Chi H.; Kalverda, Arnout P.; Kamp, Marc W. van der; Hemsworth, G.R.; Berry, Alexandria H.

doi:10.1107/s2052252519012399

Cited by 9 publications

(7 citation statements)

References 73 publications

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“…We first identified several protein domains that have been reported to form oligomers of defined sizes in vitro ( Figures S1A and S1B ; Bolten et al, 2016 ; Boudko et al, 2009 ; Büttner et al, 2012 ; Chik et al, 2019 ; Drulyte et al, 2019 ; Huang et al, 2014 ; Lee et al, 1968 ; Li et al, 2019 ; Luo et al, 2001 ; Parsons et al, 2002 ; Santiago-Frangos et al, 2019 ; Sun et al, 2014 ; Thomson et al, 2014 ; Veesler et al, 2010 ). Each oligomerization domain was tagged with a fluorescent protein and expressed in C. elegans , and the size of oligomeric protein complexes from transgenic zygotes was examined using single-cell, single-molecule pull-down (sc-SiMPull) followed by photobleaching step counting ( Dickinson et al, 2017 ; Figure S1B ).…”

Section: Resultsmentioning

confidence: 99%

A particle size threshold governs diffusion and segregation of PAR-3 during cell polarization

Chang

Dickinson

2022

Cell Reports

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Section: Resultsmentioning

confidence: 99%

A particle size threshold governs diffusion and segregation of PAR-3 during cell polarization

Chang

Dickinson

2022

Cell Reports

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“…Currently known members are PyrI4 [ 64 ], AbyU [ 65 ] and Tsn11 [ 66 ]. Moreover, further structural diversity was observed, as reports of DAases assuming a beta-barrel fold (MPS [ 32 ]), AttH-like fold (CghA [ 67 ] discussed in the next section), dimeric α + β barrel fold (StmD, NgnD and 101015D [ 64 ]), NTF2-like fold (IdmH [ 68 ]), and FAD-binding alpha/beta fold having a mixture of a 2-layer and 3-layer alpha/beta/alpha (aba) sandwich architectures (MaDA [ 63 ]) have also been reported. This observed diversity in the structures of pericyclases is thought to reflect the substantial differences in the structures of the substrates and minimal requirements for the enzyme active site to provide site-specific functional groups to catalyze pericyclic reactions.…”

Section: Pdxi/epii In Pyridoxatin/fusaricide Biosynthesis: a Turning Point Between Diels–alder And Alder-ene Reactionmentioning

confidence: 99%

Discovery and investigation of natural Diels–Alderases

Watanabe

2021

J Nat Med

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It has been proposed that biosyntheses of many natural products involve pericyclic reactions, including Diels–Alder (DA) reaction. However, only a small set of enzymes have been proposed to catalyze pericyclic reactions. Most surprisingly, there has been no formal identification of natural enzymes that can be defined to catalyze DA reactions (DAases), despite the wide application of the reaction in chemical syntheses of complex organic compounds. However, recent studies began to accumulate a growing body of evidence that supports the notion that enzymes that formally catalyze DA reactions, in fact exist. In this review, I will begin by describing a short history behind the discovery and characterization of macrophomate synthase, one of the earliest enzymes that was proposed to catalyze an intermolecular DA reaction during the biosynthesis of a substituted benzoic acid in a phytopathogenic fungus Macrophoma commelinae. Then, I will discuss representative enzymes that have been chemically authenticated to catalyze DA reactions, with emphasis on more recent discoveries of DAases involved mainly in fungal secondary metabolite biosynthesis except for one example from a marine streptomycete. The current success in identification of a series of DAases and enzymes that catalyze other pericyclic reactions owes to the combined efforts from both the experimental and theoretical approaches in discovering natural products. Such efforts typically involve identifying the chemical features derived from cycloaddition reactions, isolating the biosynthetic genes that encode enzymes that generate such chemical features and deciphering the reaction mechanisms for the enzyme-catalyzed pericyclic reactions.

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“…We tested a handful of protein domains that have been reported to autonomously organize into oligomers of defined sizes in vitro (Figure S1A-B) (Bolten et al, 2016;Boudko et al, 2009; Yiran Chang & Daniel J. Dickinson 2021, p. 2 Büttner et al, 2012;Chik et al, 2019;Drulyte et al, 2019;Huang et al, 2014;Lee et al, 1968;Li et al, 2019;Luo et al, 2001;Parsons et al, 2002;Santiago-Frangos et al, 2019;Sun et al, 2014;Thomson et al, 2014;Veesler et al, 2010). Each oligomerization domain was tagged with a fluorescent protein and expressed in C.elegans, and the size of each oligomer protein complex from the transgenic zygotes is examined using single-molecule pull-down (Sc-SiMPull) followed by photobleaching step counting (Dickinson et al, 2017).…”

Section: Engineered Par-3 Trimers Are Sufficient For Apar Segregation and Normal Developmentmentioning

confidence: 99%

A particle size threshold governs diffusion and segregation of PAR-3 during cell polarization

Chang

Dickinson

2021

Preprint

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Regulation of subcellular components' localization and motion is a critical theme in cell biology. Cells use the actomyosin cortex to regulate protein distribution on the plasma membrane, but the interplay between membrane binding, cortical movements and protein distribution remains poorly understood. In a polarizing one-cell stage Caenorhabditis elegans embryo, actomyosin flows transport PAR protein complexes into an anterior cortical domain to establish the anterior-posterior axis of the animal. Oligomerization of a key scaffold protein, PAR-3, is required for aPAR cortical localization and segregation. Although PAR-3 oligomerization is essential for polarization, it remains unclear how oligomer size contributes to aPAR segregation because PAR-3 oligomers are a heterogeneous population of many different sizes. To address this question, we engineered PAR-3 to defined sizes. We report that PAR-3 trimers are necessary and sufficient for PAR-3 function during polarization and later embryo development, while larger PAR-3 clusters are dispensable. Quantitative analysis of PAR-3 diffusion showed that PAR-3 clusters larger than a trimer are transported by viscous forces without being physically captured by the actomyosin cortex. Our study provides a quantitative model for size-dependent protein transportation of membrane proteins by cortical flow.

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Crystal structure of the putative cyclase IdmH from the indanomycin nonribosomal peptide synthase/polyketide synthase

Cited by 9 publications

References 73 publications

A particle size threshold governs diffusion and segregation of PAR-3 during cell polarization

A particle size threshold governs diffusion and segregation of PAR-3 during cell polarization

Discovery and investigation of natural Diels–Alderases

A particle size threshold governs diffusion and segregation of PAR-3 during cell polarization

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