Structural and biochemical studies of erythromycin-resistance methyltransferases : insights into structure-based drug design
Erm38 is a methyltransferase from Mycolicibacterium smegmatis that methylates the A2058 position in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor. It confers resistance to macrolides, lincosamides and streptogramins in Gram-positive bacteria and mycobacteria. In this project, we obtaine...
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| Format: | Final Year Project (FYP) |
| Language: | English |
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Nanyang Technological University
2020
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| Online Access: | https://hdl.handle.net/10356/140816 |
| _version_ | 1826120888170315776 |
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| author | Xiang, Xinyu |
| author2 | Julien Lescar |
| author_facet | Julien Lescar Xiang, Xinyu |
| author_sort | Xiang, Xinyu |
| collection | NTU |
| description | Erm38 is a methyltransferase from Mycolicibacterium smegmatis that methylates the A2058 position in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor. It confers resistance to macrolides, lincosamides and streptogramins in Gram-positive bacteria and mycobacteria. In this project, we obtained apo crystals of Erm38 and revealed its structure information. Erm38 has a N-terminal Rossmann-like α/β catalytic domain and a C-terminal helical domain. Superposition and sequence alignment revealed a highly conserved SAM-binding pocket to ErmE and ErmC in the family. We also determined the binding between Erm38 and its natural RNA substrate, with a Kd of 164nM(±36nM). We then performed fragment-based screening using Thermal Shift Assay on a library of 1000 fragments. 74 hits were identified, out of which 33 were selected and soaked into apo Erm38 crystals. One fragment, Fragment 26, was validated by X-ray Crystallography and its crystal structure determined to 2.3A resolution. We revealed that fragment 26 binds within the SAM-binding pocket, its tail forming hydrogen bonds with residues E72 and V73, while its head interacting with L105 and other surrounding residues. A potential competitive SAM inhibitor, Fragment 26 serves as an important anchor for further optimization to increase its selectivity and binding affinity. |
| first_indexed | 2024-10-01T05:23:48Z |
| format | Final Year Project (FYP) |
| id | ntu-10356/140816 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:23:48Z |
| publishDate | 2020 |
| publisher | Nanyang Technological University |
| record_format | dspace |
| spelling | ntu-10356/1408162023-02-28T18:08:45Z Structural and biochemical studies of erythromycin-resistance methyltransferases : insights into structure-based drug design Xiang, Xinyu Julien Lescar School of Biological Sciences NTU Institute of Structural Biology SMART Peter Dedon julien@ntu.edu.sg, pcdedon@mit.edu Science::Biological sciences Erm38 is a methyltransferase from Mycolicibacterium smegmatis that methylates the A2058 position in 23S rRNA using S-adenosyl methionine (SAM) as methyl donor. It confers resistance to macrolides, lincosamides and streptogramins in Gram-positive bacteria and mycobacteria. In this project, we obtained apo crystals of Erm38 and revealed its structure information. Erm38 has a N-terminal Rossmann-like α/β catalytic domain and a C-terminal helical domain. Superposition and sequence alignment revealed a highly conserved SAM-binding pocket to ErmE and ErmC in the family. We also determined the binding between Erm38 and its natural RNA substrate, with a Kd of 164nM(±36nM). We then performed fragment-based screening using Thermal Shift Assay on a library of 1000 fragments. 74 hits were identified, out of which 33 were selected and soaked into apo Erm38 crystals. One fragment, Fragment 26, was validated by X-ray Crystallography and its crystal structure determined to 2.3A resolution. We revealed that fragment 26 binds within the SAM-binding pocket, its tail forming hydrogen bonds with residues E72 and V73, while its head interacting with L105 and other surrounding residues. A potential competitive SAM inhibitor, Fragment 26 serves as an important anchor for further optimization to increase its selectivity and binding affinity. Bachelor of Science in Biological Sciences 2020-06-02T05:36:48Z 2020-06-02T05:36:48Z 2020 Final Year Project (FYP) https://hdl.handle.net/10356/140816 en application/pdf Nanyang Technological University |
| spellingShingle | Science::Biological sciences Xiang, Xinyu Structural and biochemical studies of erythromycin-resistance methyltransferases : insights into structure-based drug design |
| title | Structural and biochemical studies of erythromycin-resistance methyltransferases : insights into structure-based drug design |
| title_full | Structural and biochemical studies of erythromycin-resistance methyltransferases : insights into structure-based drug design |
| title_fullStr | Structural and biochemical studies of erythromycin-resistance methyltransferases : insights into structure-based drug design |
| title_full_unstemmed | Structural and biochemical studies of erythromycin-resistance methyltransferases : insights into structure-based drug design |
| title_short | Structural and biochemical studies of erythromycin-resistance methyltransferases : insights into structure-based drug design |
| title_sort | structural and biochemical studies of erythromycin resistance methyltransferases insights into structure based drug design |
| topic | Science::Biological sciences |
| url | https://hdl.handle.net/10356/140816 |
| work_keys_str_mv | AT xiangxinyu structuralandbiochemicalstudiesoferythromycinresistancemethyltransferasesinsightsintostructurebaseddrugdesign |