1
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Stolyarchuk M, Botnari M, Tchertanov L. Vitamin K Epoxide Reductase Complex-Protein Disulphide Isomerase Assemblies in the Thiol-Disulphide Exchange Reactions: Portrayal of Precursor-to-Successor Complexes. Int J Mol Sci 2024; 25:4135. [PMID: 38673722 PMCID: PMC11050172 DOI: 10.3390/ijms25084135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The human Vitamin K Epoxide Reductase Complex (hVKORC1), a key enzyme that converts vitamin K into the form necessary for blood clotting, requires for its activation the reducing equivalents supplied by its redox partner through thiol-disulphide exchange reactions. The functionally related molecular complexes assembled during this process have never been described, except for a proposed de novo model of a 'precursor' complex of hVKORC1 associated with protein disulphide isomerase (PDI). Using numerical approaches (in silico modelling and molecular dynamics simulation), we generated alternative 3D models for each molecular complex bonded either covalently or non-covalently. These models differ in the orientation of the PDI relative to hVKORC1 and in the cysteine residue involved in forming protein-protein disulphide bonds. Based on a comparative analysis of these models' shape, folding, and conformational dynamics, the most probable putative complexes, mimicking the 'precursor', 'intermediate', and 'successor' states, were suggested. In addition, we propose using these complexes to develop the 'allo-network drugs' necessary for treating blood diseases.
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Affiliation(s)
| | | | - Luba Tchertanov
- Centre Borelli, ENS Paris-Saclay, CNRS, Université Paris-Saclay, 4 Avenue des Sciences, 91190 Gif-sur-Yvette, France; (M.S.); (M.B.)
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2
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Li S, Sun J, Liu S, Zhou F, Gross ML, Li W. Missense VKOR mutants exhibit severe warfarin resistance but lack VKCFD via shifting to an aberrantly reduced state. Blood Adv 2023; 7:2271-2282. [PMID: 36508285 PMCID: PMC10225482 DOI: 10.1182/bloodadvances.2021006876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 12/14/2022] Open
Abstract
Missense vitamin K epoxide reductase (VKOR) mutations in patients cause resistance to warfarin treatment but not abnormal bleeding due to defective VKOR activity. The underlying mechanism of these phenotypes remains unknown. Here we show that the redox state of these mutants is essential to their activity and warfarin resistance. Using a mass spectrometry-based footprinting method, we found that severe warfarin-resistant mutations change the VKOR active site to an aberrantly reduced state in cells. Molecular dynamics simulation based on our recent crystal structures of VKOR reveals that these mutations induce an artificial opening of the protein conformation that increases access of small molecules, enabling them to reduce the active site and generating constitutive activity uninhibited by warfarin. Increased activity also compensates for the weakened substrate binding caused by these mutations, thereby maintaining normal VKOR function. The uninhibited nature of severe resistance mutations suggests that patients showing signs of such mutations should be treated by alternative anticoagulation strategies.
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Affiliation(s)
- Shuang Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | - Jie Sun
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO
| | - Shixuan Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | - Fengbo Zhou
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
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3
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Li W. Distinct enzymatic strategies for de novo generation of disulfide bonds in membranes. Crit Rev Biochem Mol Biol 2023; 58:36-49. [PMID: 37098102 PMCID: PMC10460286 DOI: 10.1080/10409238.2023.2201404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/02/2023] [Accepted: 04/06/2023] [Indexed: 04/26/2023]
Abstract
Disulfide bond formation is a catalyzed reaction essential for the folding and stability of proteins in the secretory pathway. In prokaryotes, disulfide bonds are generated by DsbB or VKOR homologs that couple the oxidation of a cysteine pair to quinone reduction. Vertebrate VKOR and VKOR-like enzymes have gained the epoxide reductase activity to support blood coagulation. The core structures of DsbB and VKOR variants share the architecture of a four-transmembrane-helix bundle that supports the coupled redox reaction and a flexible region containing another cysteine pair for electron transfer. Despite considerable similarities, recent high-resolution crystal structures of DsbB and VKOR variants reveal significant differences. DsbB activates the cysteine thiolate by a catalytic triad of polar residues, a reminiscent of classical cysteine/serine proteases. In contrast, bacterial VKOR homologs create a hydrophobic pocket to activate the cysteine thiolate. Vertebrate VKOR and VKOR-like maintain this hydrophobic pocket and further evolved two strong hydrogen bonds to stabilize the reaction intermediates and increase the quinone redox potential. These hydrogen bonds are critical to overcome the higher energy barrier required for epoxide reduction. The electron transfer process of DsbB and VKOR variants uses slow and fast pathways, but their relative contribution may be different in prokaryotic and eukaryotic cells. The quinone is a tightly bound cofactor in DsbB and bacterial VKOR homologs, whereas vertebrate VKOR variants use transient substrate binding to trigger the electron transfer in the slow pathway. Overall, the catalytic mechanisms of DsbB and VKOR variants have fundamental differences.
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Affiliation(s)
- Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
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4
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Liu S, Shen G, Li W. Structural and cellular basis of vitamin K antagonism. J Thromb Haemost 2022; 20:1971-1983. [PMID: 35748323 DOI: 10.1111/jth.15800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/30/2022]
Abstract
Vitamin K antagonists (VKAs), such as warfarin, are oral anticoagulants widely used to treat and prevent thromboembolic diseases. Therapeutic use of these drugs requires frequent monitoring and dose adjustments, whereas overdose often causes severe bleeding. Addressing these drawbacks requires mechanistic understandings at cellular and structural levels. As the target of VKAs, vitamin K epoxide reductase (VKOR) generates the active, hydroquinone form of vitamin K, which in turn drives the γ-carboxylation of several coagulation factors required for their activity. Crystal structures revealed that VKAs inhibit VKOR via mimicking its catalytic process. At the active site, two strong hydrogen bonds that facilitate the catalysis also afford the binding specificity for VKAs. Binding of VKAs induces a global change from open to closed conformation. Similar conformational change is induced by substrate binding to promote an electron transfer process that reduces the VKOR active site. In the cellular environment, reducing partner proteins or small reducing molecules may afford electrons to maintain the VKOR activity. The catalysis and VKA inhibition require VKOR in different cellular redox states, explaining the complex kinetics behavior of VKAs. Recent studies also revealed the mechanisms underlying warfarin resistance, warfarin dose variation, and antidoting by vitamin K. These mechanistic understandings may lead to improved anticoagulation strategies targeting the vitamin K cycle.
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Affiliation(s)
- Shixuan Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Guomin Shen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Henan International Joint Laboratory of Thrombosis and Hemostasis, School of Basic Medical Science, Henan University of Science and Technology, Luoyang, China
- Department of Cell Biology, Harbin Medical University, Harbin, China
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
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5
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Cheng M, Guo C, Li W, Gross ML. Free-Radical Membrane Protein Footprinting by Photolysis of Perfluoroisopropyl Iodide Partitioned to Detergent Micelle by Sonication. Angew Chem Int Ed Engl 2021; 60:8867-8873. [PMID: 33751812 PMCID: PMC8083173 DOI: 10.1002/anie.202014096] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/29/2020] [Indexed: 12/14/2022]
Abstract
A free-radical footprinting approach is described for integral membrane protein (IMP) that extends, significantly, the "fast photochemical oxidation of proteins" (FPOP) platform. This new approach exploits highly hydrophobic perfluoroisopropyl iodide (PFIPI) together with tip sonication to ensure efficient transport into the micelle interior, allowing laser dissociation and footprinting of the transmembrane domains. In contrast to water soluble footprinters, PFIPI footprints both the hydrophobic intramembrane and the hydrophilic extramembrane domains of the IMP vitamin K epoxide reductase (VKOR). The footprinting is fast, giving high coverage for Tyr (100 %) and Trp. The incorporation of the reagent with sonication does not significantly affect VKOR's enzymatic function, and tyrosine iodination does not compromise protease digestion and the subsequent analysis. The locations for the modifications are largely consistent with the corresponding solvent accessibilities, recommending this approach for future membrane protein footprinting.
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Affiliation(s)
- Ming Cheng
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
- Current address: Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chunyang Guo
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
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6
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Shen G, Cui W, Cao Q, Gao M, Liu H, Su G, Gross ML, Li W. The catalytic mechanism of vitamin K epoxide reduction in a cellular environment. J Biol Chem 2021; 296:100145. [PMID: 33273012 PMCID: PMC7895805 DOI: 10.1074/jbc.ra120.015401] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/28/2020] [Accepted: 12/03/2020] [Indexed: 11/06/2022] Open
Abstract
Vitamin K epoxide reductases (VKORs) constitute a major family of integral membrane thiol oxidoreductases. In humans, VKOR sustains blood coagulation and bone mineralization through the vitamin K cycle. Previous chemical models assumed that the catalysis of human VKOR (hVKOR) starts from a fully reduced active site. This state, however, constitutes only a minor cellular fraction (5.6%). Thus, the mechanism whereby hVKOR catalysis is carried out in the cellular environment remains largely unknown. Here we use quantitative mass spectrometry (MS) and electrophoretic mobility analyses to show that KO likely forms a covalent complex with a cysteine mutant mimicking hVKOR in a partially oxidized state. Trapping of this potential reaction intermediate suggests that the partially oxidized state is catalytically active in cells. To investigate this activity, we analyze the correlation between the cellular activity and the cellular cysteine status of hVKOR. We find that the partially oxidized hVKOR has considerably lower activity than hVKOR with a fully reduced active site. Although there are more partially oxidized hVKOR than fully reduced hVKOR in cells, these two reactive states contribute about equally to the overall hVKOR activity, and hVKOR catalysis can initiate from either of these states. Overall, the combination of MS quantification and biochemical analyses reveals the catalytic mechanism of this integral membrane enzyme in a cellular environment. Furthermore, these results implicate how hVKOR is inhibited by warfarin, one of the most commonly prescribed drugs.
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Affiliation(s)
- Guomin Shen
- Henan International Joint Laboratory of Thrombosis and Hemostasis, School of Basic Medical Science, Henan University of Science and Technology, Luoyang, Henan, China; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, USA.
| | - Weidong Cui
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA
| | - Qing Cao
- Henan International Joint Laboratory of Thrombosis and Hemostasis, School of Basic Medical Science, Henan University of Science and Technology, Luoyang, Henan, China
| | - Meng Gao
- Henan International Joint Laboratory of Thrombosis and Hemostasis, School of Basic Medical Science, Henan University of Science and Technology, Luoyang, Henan, China
| | - Hongli Liu
- Henan International Joint Laboratory of Thrombosis and Hemostasis, School of Basic Medical Science, Henan University of Science and Technology, Luoyang, Henan, China
| | - Gaigai Su
- Henan International Joint Laboratory of Thrombosis and Hemostasis, School of Basic Medical Science, Henan University of Science and Technology, Luoyang, Henan, China
| | - Michael L Gross
- Department of Chemistry, Washington University in St Louis, St Louis, Missouri, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, Missouri, USA.
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7
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Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS, Rettie AE, Fowler DM. Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. eLife 2020; 9:e58026. [PMID: 32870157 PMCID: PMC7462613 DOI: 10.7554/elife.58026] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/28/2020] [Indexed: 01/05/2023] Open
Abstract
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.
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Affiliation(s)
- Melissa A Chiasson
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Nathan J Rollins
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Jason J Stephany
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Katherine A Sitko
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Kenneth A Matreyek
- Department of Genome Sciences, University of WashingtonSeattleUnited States
| | - Marta Verby
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Song Sun
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, and Lunenfeld-Tanenbaum Research Institute, Sinai Health SystemTorontoCanada
| | | | - Debora S Marks
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of WashingtonSeattleUnited States
| | - Douglas M Fowler
- Department of Genome Sciences, University of WashingtonSeattleUnited States
- Department of Bioengineering, University of WashingtonSeattleUnited States
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8
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Beato S, Marques C, Laizé V, Gavaia PJ, Fernández I. New Insights on Vitamin K Metabolism in Senegalese sole ( Solea senegalensis) Based on Ontogenetic and Tissue-Specific Vitamin K Epoxide Reductase Molecular Data. Int J Mol Sci 2020; 21:E3489. [PMID: 32429051 PMCID: PMC7278968 DOI: 10.3390/ijms21103489] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
Vitamin K (VK) is a key nutrient for several biological processes (e.g., blood clotting and bone metabolism). To fulfill VK nutritional requirements, VK action as an activator of pregnane X receptor (Pxr) signaling pathway, and as a co-factor of γ-glutamyl carboxylase enzyme, should be considered. In this regard, VK recycling through vitamin K epoxide reductases (Vkors) is essential and should be better understood. Here, the expression patterns of vitamin K epoxide reductase complex subunit 1 (vkorc1) and vkorc1 like 1 (vkorc1l1) were determined during the larval ontogeny of Senegalese sole (Solea senegalensis), and in early juveniles cultured under different physiological conditions. Full-length transcripts for ssvkorc1 and ssvkorc1l1 were determined and peptide sequences were found to be evolutionarily conserved. During larval development, expression of ssvkorc1 showed a slight increase during absence or low feed intake. Expression of ssvkorc1l1 continuously decreased until 24 h post-fertilization, and remained constant afterwards. Both ssvkors were ubiquitously expressed in adult tissues, and highest expression was found in liver for ssvkorc1, and ovary and brain for ssvkorc1l1. Expression of ssvkorc1 and ssvkorc1l1 was differentially regulated under physiological conditions related to fasting and re-feeding, but also under VK dietary supplementation and induced deficiency. The present work provides new and basic molecular clues evidencing how VK metabolism in marine fish is sensitive to nutritional and environmental conditions.
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Affiliation(s)
- Silvia Beato
- Campus de Vegazana, Universidad de León (ULE), s/n, 24071 León, Spain;
| | - Carlos Marques
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (C.M.); (V.L.); (P.J.G.)
| | - Vincent Laizé
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (C.M.); (V.L.); (P.J.G.)
| | - Paulo J. Gavaia
- Centro de Ciências do Mar (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; (C.M.); (V.L.); (P.J.G.)
- Departamento de Ciências Biomédicas e Medicina (DCBM), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Ignacio Fernández
- Center for Aquaculture Research, Agrarian Technological Institute of Castile and Leon, Ctra. Arévalo, S/n. Zamarramala, 40196 Segovia, Spain
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9
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Nakayama SMM, Morita A, Ikenaka Y, Kawai YK, Watanabe KP, Ishii C, Mizukawa H, Yohannes YB, Saito K, Watanabe Y, Ito M, Ohsawa N, Ishizuka M. Avian interspecific differences in VKOR activity and inhibition: Insights from amino acid sequence and mRNA expression ratio of VKORC1 and VKORC1L1. Comp Biochem Physiol C Toxicol Pharmacol 2020; 228:108635. [PMID: 31639498 DOI: 10.1016/j.cbpc.2019.108635] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/16/2019] [Accepted: 09/26/2019] [Indexed: 11/22/2022]
Abstract
Worldwide use of anticoagulant rodenticides (ARs) for rodents control has frequently led to secondary poisoning of non-target animals, especially raptors. In order to suggest some factors that may help considering the mechanism of the incidents, this study focused on the avian vitamin K 2, 3-epoxide reductase (VKOR) that is the target protein of ARs. We addressed the interspecific differences in VKOR activity and inhibition related to amino acid sequence and mRNA expression of VKORC1 and VKORC1-like1 (VKORC1L1). Poultry have been considered to be more tolerant to ARs than mammals. However, VKOR activity of owls, hawks, falcon and surprisingly, canaries, was lower and inhibited by warfarin more easily than that of chickens and turkeys. The amino acid sequence of VKORC1 and VKORC1L1 implied that the value of Ki for VKOR activity to ARs could depend on the amino acid at position 140 in the TYX warfarin-binding motif in VKORC1, and other amino acid mutations in VKORC1L1. The mRNA expression ratio of VKORC1:VKORC1L1 differed between turkey (8:1) and chicken (2:3) liver. VKORC1L1 has been reported to be resistant to warfarin compared to VKORC1. Hence, both the Ki of specific VKORC1 and VKORC1L1, and the mRNA expression ratio would cause avian interspecific difference of the VKOR inhibition. Our study also suggested the high inhibition of VKOR activities in raptors and surprisingly that in canaries as well. These factors are the most likely to contribute to the high sensitivity to ARs found in raptors.
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Affiliation(s)
- Shouta M M Nakayama
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Kita18, Nishi9, Kita-ku, Sapporo 060-0818, Japan
| | - Ayuko Morita
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Kita18, Nishi9, Kita-ku, Sapporo 060-0818, Japan
| | - Yoshinori Ikenaka
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Kita18, Nishi9, Kita-ku, Sapporo 060-0818, Japan; Water Research Group, Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Yusuke K Kawai
- Diagnostic Center for Animal Health and Food Safety, Obihiro University of Agriculture and Veterinary Medicine, Obihiro 080-8555, Japan
| | - Kensuke P Watanabe
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Kita18, Nishi9, Kita-ku, Sapporo 060-0818, Japan
| | - Chihiro Ishii
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Kita18, Nishi9, Kita-ku, Sapporo 060-0818, Japan
| | - Hazuki Mizukawa
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Kita18, Nishi9, Kita-ku, Sapporo 060-0818, Japan
| | - Yared B Yohannes
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Kita18, Nishi9, Kita-ku, Sapporo 060-0818, Japan
| | - Keisuke Saito
- Institute for Raptor Biomedicine Japan 2-2101, Hokuto, Kushiro-shi, Hokkaido 084-0922, Japan
| | - Yukiko Watanabe
- Institute for Raptor Biomedicine Japan 2-2101, Hokuto, Kushiro-shi, Hokkaido 084-0922, Japan
| | | | | | - Mayumi Ishizuka
- Laboratory of Toxicology, Faculty of Veterinary Medicine, Hokkaido University, Kita18, Nishi9, Kita-ku, Sapporo 060-0818, Japan.
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10
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Lacombe J, Ferron M. VKORC1L1, An Enzyme Mediating the Effect of Vitamin K in Liver and Extrahepatic Tissues. Nutrients 2018; 10:nu10080970. [PMID: 30050002 PMCID: PMC6116193 DOI: 10.3390/nu10080970] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/18/2018] [Accepted: 07/24/2018] [Indexed: 12/25/2022] Open
Abstract
Vitamin K is an essential nutrient involved in the regulation of blood clotting and tissue mineralization. Vitamin K oxidoreductase (VKORC1) converts vitamin K epoxide into reduced vitamin K, which acts as the co-factor for the γ-carboxylation of several proteins, including coagulation factors produced by the liver. VKORC1 is also the pharmacological target of warfarin, a widely used anticoagulant. Vertebrates possess a VKORC1 paralog, VKORC1-like 1 (VKORC1L1), but until very recently, the importance of VKORC1L1 for protein γ-carboxylation and hemostasis in vivo was not clear. Here, we first review the current knowledge on the structure, function and expression pattern of VKORC1L1, including recent data establishing that, in the absence of VKORC1, VKORC1L1 can support vitamin K-dependent carboxylation in the liver during the pre- and perinatal periods in vivo. We then provide original data showing that the partial redundancy between VKORC1 and VKORC1L1 also exists in bone around birth. Recent studies indicate that, in vitro and in cell culture models, VKORC1L1 is less sensitive to warfarin than VKORC1. Genetic evidence is presented here, which supports the notion that VKORC1L1 is not the warfarin-resistant vitamin K quinone reductase present in the liver. In summary, although the exact physiological function of VKORC1L1 remains elusive, the latest findings clearly established that this enzyme is a vitamin K oxidoreductase, which can support γ-carboxylation in vivo.
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Affiliation(s)
- Julie Lacombe
- Integrative and Molecular Physiology research unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada.
| | - Mathieu Ferron
- Integrative and Molecular Physiology research unit, Institut de Recherches Cliniques de Montréal, Montréal, QC H2W 1R7, Canada.
- Department of Medicine and Molecular Biology Programs of the Faculty of Medicine, Université de Montréal, QC H3C 3J7, Canada.
- Division of Experimental Medicine, McGill University, Montréal, QC H4A 3J1, Canada.
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11
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Shen G, Li S, Cui W, Liu S, Liu Q, Yang Y, Gross M, Li W. Stabilization of warfarin-binding pocket of VKORC1 and VKORL1 by a peripheral region determines their different sensitivity to warfarin inhibition. J Thromb Haemost 2018; 16:1164-1175. [PMID: 29665197 PMCID: PMC6231229 DOI: 10.1111/jth.14127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Indexed: 11/30/2022]
Abstract
Essentials VKORL1 and VKORC1 have a similar overall structure and warfarin-binding pocket. A peripheral region stabilizing this pocket controls warfarin sensitivity of the VKOR paralogs. A human single nucleotide polymorphism in this region renders VKORL1 sensitive to warfarin. A group of warfarin-resistant mutations in VKORC1 acts by disrupting peripheral interactions. SUMMARY Background The human genome encodes two paralogs of vitamin-K-epoxide reductase, VKORC1 and VKORL1, that support blood coagulation and other vitamin-K-dependent processes. Warfarin inhibits both enzymes, but VKORL1 is relatively resistant to warfarin. Objectives To understand the difference between VKORL1 and VKORC1, and the cause of warfarin-resistant (WR) mutations in VKORC1. Methods We performed systematic mutagenesis and analyzed warfarin responses with a cell-based activity assay. Mass spectrometry analyses were used to detect cellular redox state. Results VKORC1 and VKORL1 adopt a similar intracellular redox state with four-transmembrane-helix topology. Most WR mutations identified in VKORC1 also confer resistance in VKORL1, indicating that warfarin inhibits these paralogs at a common binding site. A group of WR mutations, distant from the warfarin-binding site, show significantly less resistance in VKORL1 than in VKORC1, implying that their different warfarin responses are determined by peripheral interactions. Remarkably, we identify a critical peripheral region in which single mutations, Glu37Lys or His46Tyr, drastically increase the warfarin sensitivity of VKORL1. In the background of these warfarin-sensitive VKORL1 mutants, WR mutations showing relative less resistance in wild-type VKORL1 become much more resistant, suggesting a structural conversion to resemble VKORC1. At this peripheral region, we also identified a human single nucleotide polymorphism that confers warfarin sensitivity of VKORL1. Conclusions Peripheral regions of VKORC1 and VKORL1 primarily maintain the stability of their common warfarin-binding pocket, and differences of such interactions determine their relative sensitivity to warfarin inhibition. This new model also explains most WR mutations located at the peripheral regions of VKORC1.
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Affiliation(s)
- G Shen
- Institute of Hemostasis and Thrombosis, College of Medicine, Henan University of Science and Technology, Luoyang, Henan, China
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - S Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - W Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - S Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Q Liu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Y Yang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - M Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - W Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
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12
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Abstract
Vitamin K-dependent proteins require carboxylation of certain glutamates for their biological functions. The enzymes involved in the vitamin K-dependent carboxylation include: gamma-glutamyl carboxylase (GGCX), vitamin K epoxide reductase (VKOR) and an as-yet-unidentified vitamin K reductase (VKR). Due to the hydrophobicity of vitamin K, these enzymes are likely to be integral membrane proteins that reside in the endoplasmic reticulum. Therefore, structure-function studies on these enzymes have been challenging, and some of the results are notably controversial. Patients with naturally occurring mutations in these enzymes, who mainly exhibit bleeding disorders or are resistant to oral anticoagulant treatment, provide valuable information for the functional study of the vitamin K cycle enzymes. In this review, we discuss: (i) the discovery of the enzymatic activities and gene identifications of the vitamin K cycle enzymes; (ii) the identification of their functionally important regions and their active site residues; (iii) the membrane topology studies of GGCX and VKOR; and (iv) the controversial issues regarding the structure and function studies of these enzymes, particularly, the membrane topology, the role of the conserved cysteines and the mechanism of active site regeneration of VKOR. We also discuss the possibility that a paralogous protein of VKOR, VKOR-like 1 (VKORL1), is involved in the vitamin K cycle, and the importance of and possible approaches for identifying the unknown VKR. Overall, we describe the accomplishments and the remaining questions in regard to the structure and function studies of the enzymes in the vitamin K cycle.
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Affiliation(s)
- J-K Tie
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - D W Stafford
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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13
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Bevans CG, Krettler C, Reinhart C, Watzka M, Oldenburg J. Phylogeny of the Vitamin K 2,3-Epoxide Reductase (VKOR) Family and Evolutionary Relationship to the Disulfide Bond Formation Protein B (DsbB) Family. Nutrients 2015; 7:6224-49. [PMID: 26230708 PMCID: PMC4555120 DOI: 10.3390/nu7085281] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 06/25/2015] [Accepted: 07/09/2015] [Indexed: 12/04/2022] Open
Abstract
In humans and other vertebrate animals, vitamin K 2,3-epoxide reductase (VKOR) family enzymes are the gatekeepers between nutritionally acquired K vitamins and the vitamin K cycle responsible for posttranslational modifications that confer biological activity upon vitamin K-dependent proteins with crucial roles in hemostasis, bone development and homeostasis, hormonal carbohydrate regulation and fertility. We report a phylogenetic analysis of the VKOR family that identifies five major clades. Combined phylogenetic and site-specific conservation analyses point to clade-specific similarities and differences in structure and function. We discovered a single-site determinant uniquely identifying VKOR homologs belonging to human pathogenic, obligate intracellular prokaryotes and protists. Building on previous work by Sevier et al. (Protein Science 14:1630), we analyzed structural data from both VKOR and prokaryotic disulfide bond formation protein B (DsbB) families and hypothesize an ancient evolutionary relationship between the two families where one family arose from the other through a gene duplication/deletion event. This has resulted in circular permutation of primary sequence threading through the four-helical bundle protein folds of both families. This is the first report of circular permutation relating distant α-helical membrane protein sequences and folds. In conclusion, we suggest a chronology for the evolution of the five extant VKOR clades.
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Affiliation(s)
| | - Christoph Krettler
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60388 Frankfurt am Main, Germany.
| | - Christoph Reinhart
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, 60388 Frankfurt am Main, Germany.
| | - Matthias Watzka
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, 53105 Bonn, Germany.
| | - Johannes Oldenburg
- Institute of Experimental Haematology and Transfusion Medicine, University Clinic Bonn, 53105 Bonn, Germany.
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14
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Affiliation(s)
- S Wu
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
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15
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Premkumar L, Heras B, Duprez W, Walden P, Halili M, Kurth F, Fairlie DP, Martin JL. Rv2969c, essential for optimal growth in Mycobacterium tuberculosis, is a DsbA-like enzyme that interacts with VKOR-derived peptides and has atypical features of DsbA-like disulfide oxidases. Acta Crystallogr D Biol Crystallogr 2013; 69:1981-94. [PMID: 24100317 PMCID: PMC3792642 DOI: 10.1107/s0907444913017800] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 06/28/2013] [Indexed: 12/16/2022]
Abstract
The bacterial disulfide machinery is an attractive molecular target for developing new antibacterials because it is required for the production of multiple virulence factors. The archetypal disulfide oxidase proteins in Escherichia coli (Ec) are DsbA and DsbB, which together form a functional unit: DsbA introduces disulfides into folding proteins and DsbB reoxidizes DsbA to maintain it in the active form. In Mycobacterium tuberculosis (Mtb), no DsbB homologue is encoded but a functionally similar but structurally divergent protein, MtbVKOR, has been identified. Here, the Mtb protein Rv2969c is investigated and it is shown that it is the DsbA-like partner protein of MtbVKOR. It is found that it has the characteristic redox features of a DsbA-like protein: a highly acidic catalytic cysteine, a highly oxidizing potential and a destabilizing active-site disulfide bond. Rv2969c also has peptide-oxidizing activity and recognizes peptide segments derived from the periplasmic loops of MtbVKOR. Unlike the archetypal EcDsbA enzyme, Rv2969c has little or no activity in disulfide-reducing and disulfide-isomerase assays. The crystal structure of Rv2969c reveals a canonical DsbA fold comprising a thioredoxin domain with an embedded helical domain. However, Rv2969c diverges considerably from other DsbAs, including having an additional C-terminal helix (H8) that may restrain the mobility of the catalytic helix H1. The enzyme is also characterized by a very shallow hydrophobic binding surface and a negative electrostatic surface potential surrounding the catalytic cysteine. The structure of Rv2969c was also used to model the structure of a paralogous DsbA-like domain of the Ser/Thr protein kinase PknE. Together, these results show that Rv2969c is a DsbA-like protein with unique properties and a limited substrate-binding specificity.
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Affiliation(s)
- Lakshmanane Premkumar
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Begoña Heras
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Wilko Duprez
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Patricia Walden
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Maria Halili
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Fabian Kurth
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - David P. Fairlie
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
| | - Jennifer L. Martin
- Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, St Lucia, QLD 4067, Australia
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