Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase
Abstract Enzymes from salt-in halophiles are stable in conditions of low water activity with applications in chiral synthesis requiring organic solvents, yet the origins of such stability remains poorly understood. Here we describe the molecular basis of the reaction mechanism and dual NADH/NADPH-sp...
Saved in:
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-08-01
|
| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08587-7 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849342326841802752 |
|---|---|
| author | Jessica Domenech Nuttawan Pramanpol Claudine Bisson Sveta E. Sedelnikova Joshua R. Barrett Abdul A. A. B. Dakhil Vitaliy Mykhaylyk Ali S. Abdelhameed Stephen E. Harding David W. Rice Patrick J. Baker Juan Ferrer |
| author_facet | Jessica Domenech Nuttawan Pramanpol Claudine Bisson Sveta E. Sedelnikova Joshua R. Barrett Abdul A. A. B. Dakhil Vitaliy Mykhaylyk Ali S. Abdelhameed Stephen E. Harding David W. Rice Patrick J. Baker Juan Ferrer |
| author_sort | Jessica Domenech |
| collection | DOAJ |
| description | Abstract Enzymes from salt-in halophiles are stable in conditions of low water activity with applications in chiral synthesis requiring organic solvents, yet the origins of such stability remains poorly understood. Here we describe the molecular basis of the reaction mechanism and dual NADH/NADPH-specificity of D2HDH, a 2-hydroxyacid dehydrogenase from the extreme halophile Haloferax mediterranei, an organism whose proteins have to remain active in high intracellular concentrations of KCl. Halophilic adaptations of D2HDH include the expected acidic surface and a reduction in hydrophobic surface resulting from a lower lysine content. Structure determination of crystals of D2HDH grown with KCl showed that bound K+ ions were coordinated predominantly by clusters of main chain protein carbonyl ligands, with no involvement of the numerous exposed surface carboxyls. Structural comparisons identified similar sites in other halophilic proteins suggesting that the generic use of carbonyl clusters to coordinate K+ ions may also contribute in a carboxylate-independent way to the stabilisation of the folded state of the protein in its high salt environment. |
| format | Article |
| id | doaj-art-d8c682a8cbe64d9988b98dd368eee02c |
| institution | Kabale University |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-d8c682a8cbe64d9988b98dd368eee02c2025-08-20T03:43:26ZengNature PortfolioCommunications Biology2399-36422025-08-018111510.1038/s42003-025-08587-7Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenaseJessica Domenech0Nuttawan Pramanpol1Claudine Bisson2Sveta E. Sedelnikova3Joshua R. Barrett4Abdul A. A. B. Dakhil5Vitaliy Mykhaylyk6Ali S. Abdelhameed7Stephen E. Harding8David W. Rice9Patrick J. Baker10Juan Ferrer11Dept. Bioquımica y Biología Molecular y EQA. Universidad de AlicanteSchool of Biosciences, University of SheffieldSchool of Biosciences, University of SheffieldSchool of Biosciences, University of SheffieldSchool of Biosciences, University of SheffieldSchool of Biosciences, University of SheffieldDiamond Light Source, Harwell CampusNational Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, College Road, Sutton BoningtonNational Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, College Road, Sutton BoningtonSchool of Biosciences, University of SheffieldSchool of Biosciences, University of SheffieldDept. Bioquımica y Biología Molecular y EQA. Universidad de AlicanteAbstract Enzymes from salt-in halophiles are stable in conditions of low water activity with applications in chiral synthesis requiring organic solvents, yet the origins of such stability remains poorly understood. Here we describe the molecular basis of the reaction mechanism and dual NADH/NADPH-specificity of D2HDH, a 2-hydroxyacid dehydrogenase from the extreme halophile Haloferax mediterranei, an organism whose proteins have to remain active in high intracellular concentrations of KCl. Halophilic adaptations of D2HDH include the expected acidic surface and a reduction in hydrophobic surface resulting from a lower lysine content. Structure determination of crystals of D2HDH grown with KCl showed that bound K+ ions were coordinated predominantly by clusters of main chain protein carbonyl ligands, with no involvement of the numerous exposed surface carboxyls. Structural comparisons identified similar sites in other halophilic proteins suggesting that the generic use of carbonyl clusters to coordinate K+ ions may also contribute in a carboxylate-independent way to the stabilisation of the folded state of the protein in its high salt environment.https://doi.org/10.1038/s42003-025-08587-7 |
| spellingShingle | Jessica Domenech Nuttawan Pramanpol Claudine Bisson Sveta E. Sedelnikova Joshua R. Barrett Abdul A. A. B. Dakhil Vitaliy Mykhaylyk Ali S. Abdelhameed Stephen E. Harding David W. Rice Patrick J. Baker Juan Ferrer Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase Communications Biology |
| title | Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase |
| title_full | Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase |
| title_fullStr | Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase |
| title_full_unstemmed | Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase |
| title_short | Potassium binding by carbonyl clusters, halophilic adaptation and catalysis of Haloferax mediterranei D-2-hydroxyacid dehydrogenase |
| title_sort | potassium binding by carbonyl clusters halophilic adaptation and catalysis of haloferax mediterranei d 2 hydroxyacid dehydrogenase |
| url | https://doi.org/10.1038/s42003-025-08587-7 |
| work_keys_str_mv | AT jessicadomenech potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT nuttawanpramanpol potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT claudinebisson potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT svetaesedelnikova potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT joshuarbarrett potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT abdulaabdakhil potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT vitaliymykhaylyk potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT alisabdelhameed potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT stepheneharding potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT davidwrice potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT patrickjbaker potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase AT juanferrer potassiumbindingbycarbonylclustershalophilicadaptationandcatalysisofhaloferaxmediterraneid2hydroxyaciddehydrogenase |