@article{phan_manley_skirboll_cha_hilovsky_chang_thompson_liu_makris_2023, title={Excision of a Protein-Derived Amine for <i>p</i>-Aminobenzoate Assembly by the Self-Sacrificial Heterobimetallic Protein CADD}, volume={62}, ISSN={["1520-4995"]}, url={https://doi.org/10.1021/acs.biochem.3c00406}, DOI={10.1021/acs.biochem.3c00406}, abstractNote={Chlamydia protein associating with death domains (CADD), the founding member of a recently discovered class of nonheme dimetal enzymes termed hemeoxygenase-like dimetaloxidases (HDOs), plays an indispensable role in pathogen survival. CADD orchestrates the biosynthesis of p-aminobenzoic acid (pABA) for integration into folate via the self-sacrificial excision of a protein-derived tyrosine (Tyr27) and several additional processing steps, the nature and timing of which have yet to be fully clarified. Nuclear magnetic resonance (NMR) and proteomics approaches reveal the source and probable timing of amine installation by a neighboring lysine (Lys152). Turnover studies using limiting O2 have identified a para-aminobenzaldehyde (pABCHO) metabolic intermediate that is formed on the path to pABA formation. The use of pABCHO and other probe substrates shows that the heterobimetallic Fe/Mn form of the enzyme is capable of oxygen insertion to generate the pABA-carboxylate.}, number={22}, journal={BIOCHEMISTRY}, author={Phan, Han N. and Manley, Olivia M. and Skirboll, Sydney S. and Cha, Lide and Hilovsky, Dalton and Chang, Wei-chen and Thompson, Peter M. and Liu, Xiaojing and Makris, Thomas M.}, year={2023}, month={Nov}, pages={3276–3282} }
 @article{ushimaru_cha_shimo_li_paris_mori_miyamoto_coffer_uchiyama_guo_et al._2023, title={Mechanistic Analysis of Stereodivergent Nitroalkane Cyclopropanation Catalyzed by Nonheme Iron Enzymes}, volume={145}, ISSN={["1520-5126"]}, DOI={10.1021/jacs.3c08413}, abstractNote={BelL and HrmJ are α-ketoglutarate-dependent nonheme iron enzymes that catalyze the oxidative cyclization of 6-nitronorleucine, resulting in the formation of two diastereomeric 3-(2-nitrocyclopropyl)alanine (Ncpa) products containing trans-cyclopropane rings with (1'R,2'R) and (1'S,2'S) configurations, respectively. Herein, we investigate the catalytic mechanism and stereodivergency of the cyclopropanases. The results suggest that the nitroalkane moiety of the substrate is first deprotonated to produce the nitronate form. Spectroscopic analyses and biochemical assays with substrates and analogues indicate that an iron(IV)-oxo species abstracts proS-H from C4 to initiate intramolecular C-C bond formation. A hydroxylation intermediate is unlikely to be involved in the cyclopropanation reaction. Additionally, a genome mining approach is employed to discover new homologues that perform the cyclopropanation of 6-nitronorleucine to generate cis-configured Ncpa products with (1'R,2'S) or (1'S,2'R) stereochemistries. Sequence and structure comparisons of these cyclopropanases enable us to determine the amino acid residues critical for controlling the stereoselectivity of cyclopropanation.}, number={44}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Ushimaru, Richiro and Cha, Lide and Shimo, Shotaro and Li, Xiaojun and Paris, Jared C. and Mori, Takahiro and Miyamoto, Kazunori and Coffer, Lindsay and Uchiyama, Masanobu and Guo, Yisong and et al.}, year={2023}, month={Oct}, pages={24210–24217} }
 @article{cha_paris_zanella_spletzer_yao_guo_chang_2023, title={Mechanistic Studies of Aziridine Formation Catalyzed by Mononuclear Non-Heme Iron Enzymes}, volume={3}, ISSN={["1520-5126"]}, DOI={10.1021/jacs.2c12664}, abstractNote={Aziridines are compounds with a nitrogen-containing three-membered ring. When it is incorporated into natural products, the reactivity of the strained ring often drives the biological activities of aziridines. Despite its importance, the enzymes and biosynthetic strategies deployed to install this reactive moiety remain understudied. Herein, we report the use of in silico methods to identify enzymes with potential aziridine-installing (aziridinase) functionality. To validate candidates, we reconstitute enzymatic activity in vitro and demonstrate that an iron(IV)-oxo species initiates aziridine ring closure by the C-H bond cleavage. Furthermore, we divert the reaction pathway from aziridination to hydroxylation using mechanistic probes. This observation, isotope tracing experiments using H218O and 18O2, and quantitative product analysis, provide evidence for the polar capture of a carbocation species by the amine in the pathway to aziridine installation.}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Cha, Lide and Paris, Jared C. and Zanella, Brady and Spletzer, Martha and Yao, Angela and Guo, Yisong and Chang, Wei-chen}, year={2023}, month={Mar} }
 @article{wang_lu_cha_chen_palacios_li_guo_chang_chen_2023, title={Repurposing Iron- and 2-Oxoglutarate-Dependent Oxygenases to Catalyze Olefin Hydration}, volume={9}, ISSN={["1521-3773"]}, DOI={10.1002/anie.202311099}, abstractNote={Abstract}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Wang, Bingnan and Lu, Yong and Cha, Lide and Chen, Tzu-Yu and Palacios, Philip M. and Li, Liping and Guo, Yisong and Chang, Wei-chen and Chen, Chuo}, year={2023}, month={Sep} }
 @article{chen_zheng_zhang_chen_cha_tang_guo_zhou_wang_liu_et al._2022, title={Deciphering the Reaction Pathway of Mononuclear Iron Enzyme-Catalyzed N C Triple Bond Formation in Isocyanide Lipopeptide and Polyketide Biosynthesis}, volume={12}, ISSN={["2155-5435"]}, DOI={10.1021/acscatal.1c04869}, abstractNote={Despite the diversity of reactions catalyzed by 2-oxoglutarate-dependent nonheme iron (Fe/2OG) enzymes identified in recent years, only a limited number of these enzymes have been investigated in mechanistic detail. In particular, several Fe/2OG-dependent enzymes capable of catalyzing isocyanide formation have been reported. While the glycine moiety has been identified as a biosynthon for the isocyanide group, how the actual conversion is effected remains obscure. To elucidate the catalytic mechanism, we characterized two previously unidentified (AecA and AmcA) along with two known (ScoE and SfaA) Fe/2OG-dependent enzymes that catalyze N≡C triple bond installation using synthesized substrate analogues and potential intermediates. Our results indicate that isocyanide formation likely entails a two-step sequence involving an imine intermediate that undergoes decarboxylation-assisted desaturation to yield the isocyanide product. Results obtained from the in vitro experiments are further supported by mutagenesis, the product-bound enzyme structure, and in silico analysis.}, number={4}, journal={ACS CATALYSIS}, author={Chen, Tzu-Yu and Zheng, Ziyang and Zhang, Xuan and Chen, Jinfeng and Cha, Lide and Tang, Yijie and Guo, Yisong and Zhou, Jiahai and Wang, Binju and Liu, Hung-wen and et al.}, year={2022}, month={Feb}, pages={2270–2279} }
 @article{kim_chen_cha_zhou_xing_canty_zhang_chang_2022, title={Elucidation of divergent desaturation pathways in the formation of vinyl isonitrile and isocyanoacrylate}, volume={13}, ISSN={["2041-1723"]}, DOI={10.1038/s41467-022-32870-4}, abstractNote={Abstract}, number={1}, journal={NATURE COMMUNICATIONS}, author={Kim, Wantae and Chen, Tzu-Yu and Cha, Lide and Zhou, Grace and Xing, Kristi and Canty, Nicholas Koenig and Zhang, Yan and Chang, Wei-Chen}, year={2022}, month={Sep} }
 @article{manley_phan_stewart_mosley_xue_cha_bai_lightfoot_rucker_collins_et al._2022, title={Self-sacrificial tyrosine cleavage by an Fe:Mn oxygenase for the biosynthesis of para-aminobenzoate in Chlamydia trachomatis}, volume={119}, ISSN={["1091-6490"]}, url={http://dx.doi.org/10.1073/pnas.2210908119}, DOI={10.1073/pnas.2210908119}, abstractNote={
            Chlamydia protein associating with death domains (CADD) is involved in the biosynthesis of
            para
            -aminobenzoate (pABA), an essential component of the folate cofactor that is required for the survival and proliferation of the human pathogen
            Chlamydia trachomatis
            . The pathway used by
            Chlamydiae
            for pABA synthesis differs from the canonical multi-enzyme pathway used by most bacteria that relies on chorismate as a metabolic precursor. Rather, recent work showed pABA formation by CADD derives from
            l
            -tyrosine. As a member of the emerging superfamily of heme oxygenase–like diiron oxidases (HDOs), CADD was proposed to use a diiron cofactor for catalysis. However, we report maximal pABA formation by CADD occurs upon the addition of both iron and manganese, which implicates a heterobimetallic Fe:Mn cluster is the catalytically active form. Isotopic labeling experiments and proteomics studies show that CADD generates pABA from a protein-derived tyrosine (Tyr27), a residue that is ∼14 Å from the dimetal site. We propose that this self-sacrificial reaction occurs through O
            2
            activation by a probable Fe:Mn cluster through a radical relay mechanism that connects to the “substrate” Tyr, followed by amination and direct oxygen insertion. These results provide the molecular basis for pABA formation in
            C. trachomatis
            , which will inform the design of novel therapeutics.
          }, number={39}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, publisher={Proceedings of the National Academy of Sciences}, author={Manley, Olivia M. and Phan, Han N. and Stewart, Allison K. and Mosley, Dontae A. and Xue, Shan and Cha, Lide and Bai, Hongxia and Lightfoot, Veda C. and Rucker, Pierson A. and Collins, Leonard and et al.}, year={2022}, month={Sep} }
 @article{cha_milikisiyants_davidson_xue_smirnova_smirnov_guo_chang_2020, title={Alternative Reactivity of Leucine 5-Hydroxylase Using an Olefin-Containing Substrate to Construct a Substituted Piperidine Ring}, volume={59}, ISSN={["0006-2960"]}, url={https://doi.org/10.1021/acs.biochem.0c00289}, DOI={10.1021/acs.biochem.0c00289}, abstractNote={Applying enzymatic reactions to produce useful molecules is a central focus of chemical biology. Iron and 2-oxoglutarate (Fe/2OG) enzymes are found in all kingdoms of life and catalyze a broad array of oxidative transformations. Herein, we demonstrate that the activity of an Fe/2OG enzyme can be redirected when changing the targeted carbon hybridization from sp3 to sp2. During leucine 5-hydroxylase catalysis, installation of an olefin group onto the substrate redirects the Fe(IV)-oxo species reactivity from hydroxylation to asymmetric epoxidation. The resulting epoxide subsequently undergoes intramolecular cyclization to form the substituted piperidine, 2S,5S-hydroxypipecolic acid.}, number={21}, journal={BIOCHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Cha, Lide and Milikisiyants, Sergey and Davidson, Madison and Xue, Shan and Smirnova, Tatyana I and Smirnov, Alex I and Guo, Yisong and Chang, Wei-Chen}, year={2020}, month={Jun}, pages={1961–1965} }
 @article{cha_chang_2020, title={An Effective Strategy to Introduce Carbon Isotopes by Simple Swaps of CO2}, volume={2}, ISSN={["2589-5974"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85094605905&partnerID=MN8TOARS}, DOI={10.1016/j.trechm.2020.10.004}, abstractNote={A novel strategy to introduce C-isotopes at the carboxylate group has been discovered. Through ‘simple’ CO2 exchange under mild conditions, the C-isotope can be incorporated effectively and has been demonstrated in a variety of biologically important molecules. Also, this methodology is used to install a C–C bond when alternative electrophiles are employed. A novel strategy to introduce C-isotopes at the carboxylate group has been discovered. Through ‘simple’ CO2 exchange under mild conditions, the C-isotope can be incorporated effectively and has been demonstrated in a variety of biologically important molecules. Also, this methodology is used to install a C–C bond when alternative electrophiles are employed.}, number={12}, journal={TRENDS IN CHEMISTRY}, author={Cha, Lide and Chang, Wei-chen}, year={2020}, month={Dec}, pages={1040–1042} }
 @article{li_liao_tang_huang_cha_lin_lee_kurnikov_kurnikova_chang_et al._2020, title={Epoxidation Catalyzed by the Nonheme Iron(II)- and 2-Oxoglutarate-Dependent Oxygenase, AsqJ: Mechanistic Elucidation of Oxygen Atom Transfer by a Ferryl Intermediate}, volume={142}, ISSN={["1520-5126"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85083666781&partnerID=MN8TOARS}, DOI={10.1021/jacs.0c00484}, abstractNote={Mechanisms of enzymatic epoxidation via oxygen atom transfer (OAT) to an olefin moiety is mainly derived from the studies on thiolate-heme containing epoxidases, such as cytochrome P450 epoxidases. The molecular basis of epoxidation catalyzed by non-heme-iron enzymes is much less explored. Herein, we present a detailed study on epoxidation catalyzed by the non-heme iron- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase, AsqJ. The native substrate and analogs with different para substituents ranging from electron-donating groups (e.g. methoxy) to electron-withdrawing groups (e.g. trifluoromethyl) were used to probe the mechanism. The results derived from transient-state enzyme kinetics, Mössbauer spectroscopy, reaction product analysis, X-ray crystallography, density functional theory calculations and molecular dynamic simulations collectively revealed the following mechanistic insights: 1) The rapid O2 addition to the AsqJ Fe(II) center occurs with the iron-bound 2OG adopting an online-binding mode in which the C1 carboxylate group of 2OG is trans to the proximal histidine (His134) of the 2-His-1-carboxylate facial triad, instead of assuming the offline-binding mode with the C1 carboxylate group trans to the distal histidine (His211); 2) The decay rate constant of the ferryl intermediate is not strongly affected by the nature of the para substituents of the substrate during the OAT step, a reactivity behavior that is drastically different from non-heme Fe(IV)-oxo synthetic model complexes; 3) The OAT step most likely proceeds through a step-wise process with the initial formation of C(benzylic)-O bond to generate an Fe(III)-alkoxide species, which is observed in the AsqJ crystal structure. The subsequent C3-O bond formation completes the epoxide installation.}, number={13}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Li, Jikun and Liao, Hsuan-Jen and Tang, Yijie and Huang, Jhih-Liang and Cha, Lide and Lin, Te-Sheng and Lee, Justin L. and Kurnikov, Igor V and Kurnikova, Maria G. and Chang, Wei-Chen and et al.}, year={2020}, month={Apr}, pages={6268–6284} }
 @article{yu_tang_cha_milikisiyants_smirnova_smirnov_guo_chang_2018, title={Elucidating the Reaction Pathway of Decarboxylation-Assisted Olefination Catalyzed by a Mononuclear Non-Heme Iron Enzyme}, volume={140}, ISSN={["1520-5126"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85056414780&partnerID=MN8TOARS}, DOI={10.1021/jacs.8b10077}, abstractNote={Installation of olefins into molecules is a key transformation in organic synthesis. The recently discovered decarboxylation-assisted olefination in the biosynthesis of rhabduscin by a mononuclear non-heme iron enzyme ( P.IsnB) represents a novel approach in olefin construction. This method is commonly employed in natural product biosynthesis. Herein, we demonstrate that a ferryl intermediate is used for C-H activation at the benzylic position of the substrate. We further establish that P.IsnB reactivity can be switched from olefination to hydroxylation using electron-withdrawing groups appended on the phenyl moiety of the analogues. These experimental observations imply that a pathway involving an initial C-H activation followed by a benzylic carbocation species or by electron transfer coupled β-scission is likely utilized to complete C═C bond formation.}, number={45}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Yu, Cheng-Ping and Tang, Yijie and Cha, Lide and Milikisiyants, Sergey and Smirnova, Tatyana I. and Smirnov, Alex I. and Guo, Yisong and Chang, Wei-chen}, year={2018}, month={Nov}, pages={15190–15193} }