Crystal Structure and Sequence Analysis of N<sup>5</sup>, N<sup>10</sup>-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from <i>Porphyromonas gingivalis</i>
The methylenetetrahydrofolate dehydrogenase–cyclohydrolase (FolD) enzyme has a dual activity of N5,N10-methylenetetrahydrofolate dehydrogenase and cyclohydrolase. This enzyme plays a critical role in the chemical modification of tetrahydrofolate, which is an important coenzyme involved in the synthe...
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MDPI AG
2023-10-01
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| author | Sehyeok Im Hackwon Do Jisub Hwang Youn-Soo Shim Jun Hyuck Lee |
| author_facet | Sehyeok Im Hackwon Do Jisub Hwang Youn-Soo Shim Jun Hyuck Lee |
| author_sort | Sehyeok Im |
| collection | DOAJ |
| description | The methylenetetrahydrofolate dehydrogenase–cyclohydrolase (FolD) enzyme has a dual activity of N5,N10-methylenetetrahydrofolate dehydrogenase and cyclohydrolase. This enzyme plays a critical role in the chemical modification of tetrahydrofolate, which is an important coenzyme involved in the synthesis of DNA, RNA, and amino acids. Therefore, bacterial FolD has been studied as a potential drug target for the development of antibiotics. Here, we determined the crystal structure of FolD (<i>Pg</i>FolD) from the oral pathogen <i>Porphyromonas gingivalis</i> at 2.05 Å resolution using the molecular replacement method. The crystal structure of <i>Pg</i>FolD was successfully refined to a crystallographic R-factor of 21.4% (R<sub>free</sub> = 23.8%). The crystals belong to the space group of <i>P</i>4<sub>3</sub>22 with the unit cell parameters of a = 110.7 Å, b = 110.7 Å, and c = 69.8 Å, containing one subunit in the asymmetric unit. Our analytical size-exclusion chromatography results indicated that <i>Pg</i>FolD forms a stable dimer in solution. Additionally, structural and sequence comparison studies with previously known FolDs revealed that <i>Pg</i>FolD has a different substrate-binding site residue composition. These findings provide valuable insights for the structure-based development of specific inhibitors against the <i>Porphyromonas gingivalis</i> pathogen. |
| first_indexed | 2024-03-10T21:20:09Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2073-4352 |
| language | English |
| last_indexed | 2024-03-10T21:20:09Z |
| publishDate | 2023-10-01 |
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| series | Crystals |
| spelling | doaj.art-eb91bada6996459b80be6448840039dd2023-11-19T16:09:58ZengMDPI AGCrystals2073-43522023-10-011310148910.3390/cryst13101489Crystal Structure and Sequence Analysis of N<sup>5</sup>, N<sup>10</sup>-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from <i>Porphyromonas gingivalis</i>Sehyeok Im0Hackwon Do1Jisub Hwang2Youn-Soo Shim3Jun Hyuck Lee4Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of KoreaResearch Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of KoreaResearch Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of KoreaDepartment of Dental Hygiene, Sunmoon University, Asan 31460, Republic of KoreaResearch Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of KoreaThe methylenetetrahydrofolate dehydrogenase–cyclohydrolase (FolD) enzyme has a dual activity of N5,N10-methylenetetrahydrofolate dehydrogenase and cyclohydrolase. This enzyme plays a critical role in the chemical modification of tetrahydrofolate, which is an important coenzyme involved in the synthesis of DNA, RNA, and amino acids. Therefore, bacterial FolD has been studied as a potential drug target for the development of antibiotics. Here, we determined the crystal structure of FolD (<i>Pg</i>FolD) from the oral pathogen <i>Porphyromonas gingivalis</i> at 2.05 Å resolution using the molecular replacement method. The crystal structure of <i>Pg</i>FolD was successfully refined to a crystallographic R-factor of 21.4% (R<sub>free</sub> = 23.8%). The crystals belong to the space group of <i>P</i>4<sub>3</sub>22 with the unit cell parameters of a = 110.7 Å, b = 110.7 Å, and c = 69.8 Å, containing one subunit in the asymmetric unit. Our analytical size-exclusion chromatography results indicated that <i>Pg</i>FolD forms a stable dimer in solution. Additionally, structural and sequence comparison studies with previously known FolDs revealed that <i>Pg</i>FolD has a different substrate-binding site residue composition. These findings provide valuable insights for the structure-based development of specific inhibitors against the <i>Porphyromonas gingivalis</i> pathogen.https://www.mdpi.com/2073-4352/13/10/1489crystal structuredrug target<i>Pg</i>FolDX-ray crystallography |
| spellingShingle | Sehyeok Im Hackwon Do Jisub Hwang Youn-Soo Shim Jun Hyuck Lee Crystal Structure and Sequence Analysis of N<sup>5</sup>, N<sup>10</sup>-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from <i>Porphyromonas gingivalis</i> Crystals crystal structure drug target <i>Pg</i>FolD X-ray crystallography |
| title | Crystal Structure and Sequence Analysis of N<sup>5</sup>, N<sup>10</sup>-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from <i>Porphyromonas gingivalis</i> |
| title_full | Crystal Structure and Sequence Analysis of N<sup>5</sup>, N<sup>10</sup>-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from <i>Porphyromonas gingivalis</i> |
| title_fullStr | Crystal Structure and Sequence Analysis of N<sup>5</sup>, N<sup>10</sup>-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from <i>Porphyromonas gingivalis</i> |
| title_full_unstemmed | Crystal Structure and Sequence Analysis of N<sup>5</sup>, N<sup>10</sup>-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from <i>Porphyromonas gingivalis</i> |
| title_short | Crystal Structure and Sequence Analysis of N<sup>5</sup>, N<sup>10</sup>-Methylenetetrahydrofolate Dehydrogenase/Cyclohydrolase Enzyme from <i>Porphyromonas gingivalis</i> |
| title_sort | crystal structure and sequence analysis of n sup 5 sup n sup 10 sup methylenetetrahydrofolate dehydrogenase cyclohydrolase enzyme from i porphyromonas gingivalis i |
| topic | crystal structure drug target <i>Pg</i>FolD X-ray crystallography |
| url | https://www.mdpi.com/2073-4352/13/10/1489 |
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