Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact
Vitamin K epoxide reductase (VKOR) drives the vitamin K cycle, activating vitamin K-dependent blood clotting factors. VKOR is also the target of the widely used anticoagulant drug, warfarin. Despite VKOR’s pivotal role in coagulation, its structure and active site remain poorly understood. In additi...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2020-09-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/58026 |
| _version_ | 1811252873543024640 |
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| author | Melissa A Chiasson Nathan J Rollins Jason J Stephany Katherine A Sitko Kenneth A Matreyek Marta Verby Song Sun Frederick P Roth Daniel DeSloover Debora S Marks Allan E Rettie Douglas M Fowler |
| author_facet | Melissa A Chiasson Nathan J Rollins Jason J Stephany Katherine A Sitko Kenneth A Matreyek Marta Verby Song Sun Frederick P Roth Daniel DeSloover Debora S Marks Allan E Rettie Douglas M Fowler |
| author_sort | Melissa A Chiasson |
| collection | DOAJ |
| description | Vitamin K epoxide reductase (VKOR) drives the vitamin K cycle, activating vitamin K-dependent blood clotting factors. VKOR is also the target of the widely used anticoagulant drug, warfarin. Despite VKOR’s pivotal role in coagulation, its structure and active site remain poorly understood. In addition, VKOR variants can cause vitamin K-dependent clotting factor deficiency or alter warfarin response. Here, we used multiplexed, sequencing-based assays to measure the effects of 2,695 VKOR missense variants on abundance and 697 variants on activity in cultured human cells. The large-scale functional data, along with an evolutionary coupling analysis, supports a four transmembrane domain topology, with variants in transmembrane domains exhibiting strongly deleterious effects on abundance and activity. Functionally constrained regions of the protein define the active site, and we find that, of four conserved cysteines putatively critical for function, only three are absolutely required. Finally, 25% of human VKOR missense variants show reduced abundance or activity, possibly conferring warfarin sensitivity or causing disease. |
| first_indexed | 2024-04-12T16:42:10Z |
| format | Article |
| id | doaj.art-36b421f0fd264b0f97e516ab449e0b61 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T16:42:10Z |
| publishDate | 2020-09-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-36b421f0fd264b0f97e516ab449e0b612022-12-22T03:24:44ZengeLife Sciences Publications LtdeLife2050-084X2020-09-01910.7554/eLife.58026Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impactMelissa A Chiasson0https://orcid.org/0000-0002-1880-3181Nathan J Rollins1Jason J Stephany2Katherine A Sitko3Kenneth A Matreyek4Marta Verby5Song Sun6Frederick P Roth7Daniel DeSloover8Debora S Marks9https://orcid.org/0000-0001-9388-2281Allan E Rettie10Douglas M Fowler11https://orcid.org/0000-0001-7614-1713Department of Genome Sciences, University of Washington, Seattle, United StatesDepartment of Systems Biology, Harvard Medical School, Boston, United StatesDepartment of Genome Sciences, University of Washington, Seattle, United StatesDepartment of Genome Sciences, University of Washington, Seattle, United StatesDepartment of Genome Sciences, University of Washington, Seattle, United StatesDonnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, CanadaDonnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, CanadaDonnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, CanadaColor Genomics, Burlingame, United StatesDepartment of Systems Biology, Harvard Medical School, Boston, United StatesDepartment of Medicinal Chemistry, University of Washington, Seattle, United StatesDepartment of Genome Sciences, University of Washington, Seattle, United States; Department of Bioengineering, University of Washington, Seattle, United StatesVitamin K epoxide reductase (VKOR) drives the vitamin K cycle, activating vitamin K-dependent blood clotting factors. VKOR is also the target of the widely used anticoagulant drug, warfarin. Despite VKOR’s pivotal role in coagulation, its structure and active site remain poorly understood. In addition, VKOR variants can cause vitamin K-dependent clotting factor deficiency or alter warfarin response. Here, we used multiplexed, sequencing-based assays to measure the effects of 2,695 VKOR missense variants on abundance and 697 variants on activity in cultured human cells. The large-scale functional data, along with an evolutionary coupling analysis, supports a four transmembrane domain topology, with variants in transmembrane domains exhibiting strongly deleterious effects on abundance and activity. Functionally constrained regions of the protein define the active site, and we find that, of four conserved cysteines putatively critical for function, only three are absolutely required. Finally, 25% of human VKOR missense variants show reduced abundance or activity, possibly conferring warfarin sensitivity or causing disease.https://elifesciences.org/articles/58026membrane proteinpharmacogeneticsmultiplex |
| spellingShingle | Melissa A Chiasson Nathan J Rollins Jason J Stephany Katherine A Sitko Kenneth A Matreyek Marta Verby Song Sun Frederick P Roth Daniel DeSloover Debora S Marks Allan E Rettie Douglas M Fowler Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact eLife membrane protein pharmacogenetics multiplex |
| title | Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact |
| title_full | Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact |
| title_fullStr | Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact |
| title_full_unstemmed | Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact |
| title_short | Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact |
| title_sort | multiplexed measurement of variant abundance and activity reveals vkor topology active site and human variant impact |
| topic | membrane protein pharmacogenetics multiplex |
| url | https://elifesciences.org/articles/58026 |
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