101
|
Kudo F, Tokumitsu T, Eguchi T. Substrate specificity of radical S-adenosyl-l-methionine dehydratase AprD4 and its partner reductase AprD3 in the C3'-deoxygenation of aminoglycoside antibiotics. J Antibiot (Tokyo) 2016; 70:423-428. [PMID: 27599765 DOI: 10.1038/ja.2016.110] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 07/29/2016] [Accepted: 08/05/2016] [Indexed: 02/02/2023]
Abstract
A radical S-adenosyl-l-methionine dehydratase AprD4 and an NADPH-dependent reductase AprD3 are responsible for the C3'-deoxygenation of pseudodisaccharide paromamine in the biosynthesis of apramycin. These enzymes are involved in the construction of the characteristic structural motif that is not modified by 3'-phosphotransferase in aminoglycoside-resistant bacterial strains. AprD4 catalyzes the C3'-dehydration of paromamine via a radical-mediated reaction mechanism to give 4'-oxolividamine, which is then reduced by AprD3 with NADPH to afford lividamine. In the present study, the substrate specificity of this unique combination of enzymes has been investigated. AprD4 was found to recognize paromamine, neamine, kanamycin C, and kanamycin B to afford 5'-deoxyadenosine as one of products during the C3'-dehydration of aminoglycosides, but not 2'-N-acetylparomamine and paromomycin. Only paromamine and kanamycin C were converted to the corresponding C3'-deoxygenated compounds by AprD4 and AprD3. AprD3 recognizes the 4'-oxolividamine moiety, including the pseudotrisaccharide kanamycin C, and seems to reject the amino group at C6' of neamine and kanamycin B. Chirally deuterium-labeled NADPH was used to identify that that AprD3 transfers the pro-S hydrogen atom of NADPH when reducing 4'-oxolividamine to give lividamine.
Collapse
Affiliation(s)
- Fumitaka Kudo
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Tadashi Eguchi
- Department of Chemistry, Tokyo Institute of Technology, Tokyo, Japan
| |
Collapse
|
102
|
Ji X, Li Y, Xie L, Lu H, Ding W, Zhang Q. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues. Angew Chem Int Ed Engl 2016; 55:11845-8. [DOI: 10.1002/anie.201605917] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/11/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Xinjian Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Liqi Xie
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Haojie Lu
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Wei Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
| |
Collapse
|
103
|
Ji X, Li Y, Xie L, Lu H, Ding W, Zhang Q. Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Xinjian Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Yongzhen Li
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Liqi Xie
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Haojie Lu
- Department of Chemistry; Fudan University; Shanghai 200433 China
| | - Wei Ding
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations; School of Life Sciences; Lanzhou University; Lanzhou 730000 China
| | - Qi Zhang
- Department of Chemistry; Fudan University; Shanghai 200433 China
| |
Collapse
|
104
|
Dong M, Horitani M, Dzikovski B, Pandelia ME, Krebs C, Freed JH, Hoffman BM, Lin H. Organometallic Complex Formed by an Unconventional Radical S-Adenosylmethionine Enzyme. J Am Chem Soc 2016; 138:9755-8. [PMID: 27465315 DOI: 10.1021/jacs.6b04155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Pyrococcus horikoshii Dph2 (PhDph2) is an unusual radical S-adenosylmethionine (SAM) enzyme involved in the first step of diphthamide biosynthesis. It catalyzes the reaction by cleaving SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. To probe the reaction mechanism, we synthesized a SAM analogue (SAMCA), in which the ACP group of SAM is replaced with a 3-carboxyallyl group. SAMCA is cleaved by PhDph2, yielding a paramagnetic (S = 1/2) species, which is assigned to a complex formed between the reaction product, α-sulfinyl-3-butenoic acid, and the [4Fe-4S] cluster. Electron-nuclear double resonance (ENDOR) measurements with (13)C and (2)H isotopically labeled SAMCA support a π-complex between the C═C double bond of α-sulfinyl-3-butenoic acid and the unique iron of the [4Fe-4S] cluster. This is the first example of a radical SAM-related [4Fe-4S](+) cluster forming an organometallic complex with an alkene, shedding additional light on the mechanism of PhDph2 and expanding our current notions for the reactivity of [4Fe-4S] clusters in radical SAM enzymes.
Collapse
Affiliation(s)
- Min Dong
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Masaki Horitani
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Maria-Eirini Pandelia
- Department of Biochemistry, Brandeis University , Waltham, Massachusetts 02453, United States
| | - Carsten Krebs
- Department of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.,Howard Hughes Medical Institute, Cornell University , Ithaca, New York 14853, United States
| |
Collapse
|