Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen
Ketol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to under...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2021-11-01
|
| Series: | Biomolecules |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2218-273X/11/11/1679 |
| _version_ | 1797511092141817856 |
|---|---|
| author | Olivier Nicolas Lemaire Marie-Caroline Müller Jörg Kahnt Tristan Wagner |
| author_facet | Olivier Nicolas Lemaire Marie-Caroline Müller Jörg Kahnt Tristan Wagner |
| author_sort | Olivier Nicolas Lemaire |
| collection | DOAJ |
| description | Ketol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to understand their remarkable specificity towards NADH or NADPH, but also to develop antibiotics. Here, we present the first structural study on a KARI natively isolated from a methanogenic archaea. The dodecameric structure of 0.44-MDa was obtained in two different conformations, an open and close state refined to a resolution of 2.2-Å and 2.1-Å, respectively. These structures illustrate the conformational movement required for substrate and coenzyme binding. While the close state presents the complete NADP bound in front of a partially occupied Mg<sup>2+</sup>-site, the Mg<sup>2+</sup>-free open state contains a tartrate at the nicotinamide location and a bound NADP with the adenine-nicotinamide protruding out of the active site. Structural comparisons show a very high conservation of the active site environment and detailed analyses point towards few specific residues required for the dodecamerisation. These residues are not conserved in other dodecameric KARIs that stabilise their trimeric interface differently, suggesting that dodecamerisation, the cellular role of which is still unknown, might have occurred several times in the evolution of KARIs. |
| first_indexed | 2024-03-10T05:40:31Z |
| format | Article |
| id | doaj.art-abd59ecacfb74307a3e1bbb35f723d92 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T05:40:31Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-abd59ecacfb74307a3e1bbb35f723d922023-11-22T22:34:44ZengMDPI AGBiomolecules2218-273X2021-11-011111167910.3390/biom11111679Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic MethanogenOlivier Nicolas Lemaire0Marie-Caroline Müller1Jörg Kahnt2Tristan Wagner3Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, GermanyMicrobial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, GermanyCore Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, GermanyMicrobial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, GermanyKetol-acid reductoisomerase (KARI) orchestrates the biosynthesis of branched-chain amino acids, an elementary reaction in prototrophic organisms as well as a valuable process in biotechnology. Bacterial KARIs belonging to class I organise as dimers or dodecamers and were intensively studied to understand their remarkable specificity towards NADH or NADPH, but also to develop antibiotics. Here, we present the first structural study on a KARI natively isolated from a methanogenic archaea. The dodecameric structure of 0.44-MDa was obtained in two different conformations, an open and close state refined to a resolution of 2.2-Å and 2.1-Å, respectively. These structures illustrate the conformational movement required for substrate and coenzyme binding. While the close state presents the complete NADP bound in front of a partially occupied Mg<sup>2+</sup>-site, the Mg<sup>2+</sup>-free open state contains a tartrate at the nicotinamide location and a bound NADP with the adenine-nicotinamide protruding out of the active site. Structural comparisons show a very high conservation of the active site environment and detailed analyses point towards few specific residues required for the dodecamerisation. These residues are not conserved in other dodecameric KARIs that stabilise their trimeric interface differently, suggesting that dodecamerisation, the cellular role of which is still unknown, might have occurred several times in the evolution of KARIs.https://www.mdpi.com/2218-273X/11/11/1679ketol-acid reductoisomerasesmethanogenic archaeaX-ray crystallographyconformational rearrangementnative purificationoligomerisation |
| spellingShingle | Olivier Nicolas Lemaire Marie-Caroline Müller Jörg Kahnt Tristan Wagner Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen Biomolecules ketol-acid reductoisomerases methanogenic archaea X-ray crystallography conformational rearrangement native purification oligomerisation |
| title | Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen |
| title_full | Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen |
| title_fullStr | Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen |
| title_full_unstemmed | Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen |
| title_short | Structural Rearrangements of a Dodecameric Ketol-Acid Reductoisomerase Isolated from a Marine Thermophilic Methanogen |
| title_sort | structural rearrangements of a dodecameric ketol acid reductoisomerase isolated from a marine thermophilic methanogen |
| topic | ketol-acid reductoisomerases methanogenic archaea X-ray crystallography conformational rearrangement native purification oligomerisation |
| url | https://www.mdpi.com/2218-273X/11/11/1679 |
| work_keys_str_mv | AT oliviernicolaslemaire structuralrearrangementsofadodecamericketolacidreductoisomeraseisolatedfromamarinethermophilicmethanogen AT mariecarolinemuller structuralrearrangementsofadodecamericketolacidreductoisomeraseisolatedfromamarinethermophilicmethanogen AT jorgkahnt structuralrearrangementsofadodecamericketolacidreductoisomeraseisolatedfromamarinethermophilicmethanogen AT tristanwagner structuralrearrangementsofadodecamericketolacidreductoisomeraseisolatedfromamarinethermophilicmethanogen |