1
|
Jalali E, Wang F, Overbay BR, Miller MD, Shaaban KA, Ponomareva LV, Ye Q, Saghaeiannejad-Esfahani H, Bhardwaj M, Steele AD, Teijaro CN, Shen B, Van Lanen SG, She QB, Voss SR, Phillips GN, Thorson JS. Biochemical and Structural Studies of the Carminomycin 4- O-Methyltransferase DnrK. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38412432 DOI: 10.1021/acs.jnatprod.3c00947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Structural and functional studies of the carminomycin 4-O-methyltransferase DnrK are described, with an emphasis on interrogating the acceptor substrate scope of DnrK. Specifically, the evaluation of 100 structurally and functionally diverse natural products and natural product mimetics revealed an array of pharmacophores as productive DnrK substrates. Representative newly identified DnrK substrates from this study included anthracyclines, angucyclines, anthraquinone-fused enediynes, flavonoids, pyranonaphthoquinones, and polyketides. The ligand-bound structure of DnrK bound to a non-native fluorescent hydroxycoumarin acceptor, 4-methylumbelliferone, along with corresponding DnrK kinetic parameters for 4-methylumbelliferone and native acceptor carminomycin are also reported for the first time. The demonstrated unique permissivity of DnrK highlights the potential for DnrK as a new tool in future biocatalytic and/or strain engineering applications. In addition, the comparative bioactivity assessment (cancer cell line cytotoxicity, 4E-BP1 phosphorylation, and axolotl embryo tail regeneration) of a select set of DnrK substrates/products highlights the ability of anthracycline 4-O-methylation to dictate diverse functional outcomes.
Collapse
Affiliation(s)
| | - Fengbin Wang
- Department of Biosciences, Rice University, Houston, Texas 77030, United States
| | | | - Mitchell D Miller
- Department of Biosciences, Rice University, Houston, Texas 77030, United States
| | | | | | - Qing Ye
- Markey Cancer Center, Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | | | | | | | | | | | | | - Qing-Bai She
- Markey Cancer Center, Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - S Randal Voss
- Department of Neuroscience, University of Kentucky, Lexington, Kentucky 40536, United States
- Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky 40536, United States
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky 40536, United States
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas 77030, United States
- Department of Chemistry, Rice University, Houston, Texas 77030, United States
| | | |
Collapse
|
2
|
Dai P, Wang CX, Gao H, Wang QZ, Tang XL, Chen GD, Hong K, Hu D, Yao XS. Characterization of Methyltransferase AlmCII in Chalcomycin Biosynthesis: The First TylF Family O-Methyltransferase Works on a 4'-Deoxysugar. Chembiochem 2017; 18:1510-1517. [PMID: 28488816 DOI: 10.1002/cbic.201700216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Indexed: 11/11/2022]
Abstract
Sugar O-methylation is a ubiquitous modification in natural products and plays diverse roles. This realization has inspired many attempts to search for novel methyltransferases. Chalcomycins are a group of 16-membered macrolides containing two methylated sugars that require three methyltransferases for their biosynthesis. Here, we identified that AlmCII, a sugar O-methyltransferase belonging to the TylF family that was previously only known to methylate sugars with a 4'-hydroxy group, can methylate a 4',6'-dideoxysugar during the biosynthesis of chalcomycins. An in vitro enzymatic assay revealed that AlmCII is divalent metal-dependent with an optimal pH of 8.0 and optimal temperature of 42 °C. Moreover, the 3'-O-demethylated chalcomycins exhibit less than 6 % of the antibacterial activity of their parent compounds. This is the first report demonstrating that a TylF family O-methyltransferase can use a 4'-deoxy sugar as a substrate and highlighting the importance of this methylation for the antibacterial activity of chalcomycins.
Collapse
Affiliation(s)
- Ping Dai
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Chuan-Xi Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Hao Gao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Qiao-Zhen Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Xiao-Long Tang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, No. 185 Donghu Road, Wuhan, 430071, P. R. China
| | - Dan Hu
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, No.345 Lingling Road, Shanghai, 200032, P. R. China
| | - Xin-Sheng Yao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, No. 601 Huangpu Avenue, Guangzhou, 510632, P. R. China
| |
Collapse
|
3
|
Cao H, Tan K, Wang F, Bigelow L, Yennamalli RM, Jedrzejczak R, Babnigg G, Bingman CA, Joachimiak A, Kharel MK, Singh S, Thorson JS, Phillips GN. Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:034702. [PMID: 27191010 PMCID: PMC4851618 DOI: 10.1063/1.4948539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
CalE6 from Micromonospora echinospora is a (pyridoxal 5' phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.
Collapse
Affiliation(s)
- Hongnan Cao
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| | - Kemin Tan
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Fengbin Wang
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| | - Lance Bigelow
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | | | - Robert Jedrzejczak
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Gyorgy Babnigg
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, USA
| | - Andrzej Joachimiak
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory , Bldg. 446/Rm. A104, 970 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Madan K Kharel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - Shanteri Singh
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky , Lexington, Kentucky 40536, USA
| | - George N Phillips
- Biosciences at Rice, Rice University , 6100 Main St., Houston, Texas 77005, USA
| |
Collapse
|
4
|
Han L, Singh S, Thorson JS, Phillips GN. Loop dynamics of thymidine diphosphate-rhamnose 3'-O-methyltransferase (CalS11), an enzyme in calicheamicin biosynthesis. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:012004. [PMID: 26958582 PMCID: PMC4760980 DOI: 10.1063/1.4941368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/22/2016] [Indexed: 06/05/2023]
Abstract
Structure analysis and ensemble refinement of the apo-structure of thymidine diphosphate (TDP)-rhamnose 3'-O-methyltransferase reveal a gate for substrate entry and product release. TDP-rhamnose 3'-O-methyltransferase (CalS11) catalyses a 3'-O-methylation of TDP-rhamnose, an intermediate in the biosynthesis of enediyne antitumor antibiotic calicheamicin. CalS11 operates at the sugar nucleotide stage prior to glycosylation step. Here, we present the crystal structure of the apo form of CalS11 at 1.89 Å resolution. We propose that the L2 loop functions as a gate facilitating and/or providing specificity for substrate entry or promoting product release. Ensemble refinement analysis slightly improves the crystallographic refinement statistics and furthermore provides a compelling way to visualize the dynamic model of loop L2, supporting the understanding of its proposed role in catalysis.
Collapse
Affiliation(s)
- Lu Han
- Biosciences at Rice, Rice University , Houston, Texas 77005, USA
| | - Shanteri Singh
- Center for Pharmaceutical Research and Innovation, Pharmaceutical Sciences, University of Kentucky College of Pharmacy , Lexington, Kentucky 40536-0596, USA
| | - Jon S Thorson
- Center for Pharmaceutical Research and Innovation, Pharmaceutical Sciences, University of Kentucky College of Pharmacy , Lexington, Kentucky 40536-0596, USA
| | | |
Collapse
|
5
|
Bernard SM, Akey DL, Tripathi A, Park SR, Konwerski JR, Anzai Y, Li S, Kato F, Sherman DH, Smith JL. Structural basis of substrate specificity and regiochemistry in the MycF/TylF family of sugar O-methyltransferases. ACS Chem Biol 2015; 10:1340-51. [PMID: 25692963 DOI: 10.1021/cb5009348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates, show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homologue, active site residues were identified that correlate with the 3' or 4' specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. This classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.
Collapse
Affiliation(s)
- Steffen M. Bernard
- Chemical
Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David L. Akey
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ashootosh Tripathi
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sung Ryeol Park
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jamie R. Konwerski
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yojiro Anzai
- Faculty
of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Shengying Li
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Fumio Kato
- Faculty
of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - David H. Sherman
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Janet L. Smith
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| |
Collapse
|
6
|
Li J, Xie Z, Wang M, Ai G, Chen Y. Identification and analysis of the paulomycin biosynthetic gene cluster and titer improvement of the paulomycins in Streptomyces paulus NRRL 8115. PLoS One 2015; 10:e0120542. [PMID: 25822496 PMCID: PMC4425429 DOI: 10.1371/journal.pone.0120542] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 01/26/2015] [Indexed: 11/30/2022] Open
Abstract
The paulomycins are a group of glycosylated compounds featuring a unique paulic
acid moiety. To locate their biosynthetic gene clusters, the genomes of two
paulomycin producers, Streptomyces paulus NRRL 8115 and
Streptomyces sp. YN86, were sequenced. The paulomycin
biosynthetic gene clusters were defined by comparative analyses of the two
genomes together with the genome of the third paulomycin producer
Streptomyces albus J1074. Subsequently, the identity of the
paulomycin biosynthetic gene cluster was confirmed by inactivation of two genes
involved in biosynthesis of the paulomycose branched chain
(pau11) and the ring A moiety (pau18) in
Streptomyces paulus NRRL 8115. After determining the gene
cluster boundaries, a convergent biosynthetic model was proposed for paulomycin
based on the deduced functions of the pau genes. Finally, a
paulomycin high-producing strain was constructed by expressing an
activator-encoding gene (pau13) in S.
paulus, setting the stage for future investigations.
Collapse
Affiliation(s)
- Jine Li
- State Key Laboratory of Microbial Resources, Institute of
Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R.
China
| | - Zhoujie Xie
- State Key Laboratory of Microbial Resources, Institute of
Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R.
China
| | - Min Wang
- State Key Laboratory of Microbial Resources, Institute of
Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R.
China
| | - Guomin Ai
- State Key Laboratory of Microbial Resources, Institute of
Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R.
China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of
Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R.
China
- * E-mail:
| |
Collapse
|
7
|
Singh S, Peltier-Pain P, Tonelli M, Thorson JS. A general NMR-based strategy for the in situ characterization of sugar-nucleotide-dependent biosynthetic pathways. Org Lett 2014; 16:3220-3. [PMID: 24911465 PMCID: PMC4075999 DOI: 10.1021/ol501241a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A simple method for the study of sugar-nucleotide-dependent multienzyme cascades is highlighted where the use of selectively (13)C-labeled sugar nucleotides and inverse (13)C detection NMR offers fast, direct detection and quantification of reactants and products and circumvents the need for chromatographic separation. The utility of the method has been demonstrated by characterizing four previously uncharacterized sugar nucleotide biosynthetic enzymes involved in calicheamicin biosynthesis.
Collapse
Affiliation(s)
- Shanteri Singh
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky , 789 South Limestone Street, Lexington, Kentucky 40536, United States
| | | | | | | |
Collapse
|
8
|
Putapatri SR, Kanwal A, Sridhar B, Banerjee SK, Kantevari S. Synthesis of l-rhamnose derived chiral bicyclic triazoles as novel sodium-glucose transporter (SGLT) inhibitors. Org Biomol Chem 2014; 12:8415-21. [DOI: 10.1039/c4ob01319k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Fused chiral bicyclic 1,2,3-triazoles synthesized from commercially available natural l-rhamnose exhibited excellent SGLT inhibition activity.
Collapse
Affiliation(s)
- Siddamal Reddy Putapatri
- Organic Chemistry Division-II (C P C Division)
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India
| | - Abhinav Kanwal
- Medicinal Chemistry and Pharmacology Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India
| | - Balasubramanian Sridhar
- Laboratory of X-ray Crystallography
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India
| | - Sanjay K. Banerjee
- Medicinal Chemistry and Pharmacology Division
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India
| | - Srinivas Kantevari
- Organic Chemistry Division-II (C P C Division)
- CSIR-Indian Institute of Chemical Technology
- Hyderabad
- India
| |
Collapse
|