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Liu J, Liang P. Complexation and evolution of cis-prenyltransferase homologues in Cinnamomum kanehirae deduced from kinetic and functional characterizations. Protein Sci 2023; 32:e4828. [PMID: 37916302 PMCID: PMC10661081 DOI: 10.1002/pro.4828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/20/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Eukaryotic dehydrodolichyl diphosphate synthases (DHDDSs), cis-prenyltransferases (cis-PTs) synthesizing precursors of dolichols to mediate glycoprotein biosynthesis require partners, for eample Nus1 in yeast and NgBR in animals, which are cis-PTs homologues without activity but to boost the DHDDSs activity. Unlike animals, plants have multiple cis-PT homologues to pair or stand alone to produce various chain-length products with less known physiological roles. We chose Cinnamomum kanehirae, a tree that contains two DHDDS-like and three NgBR-like proteins from genome analysis, and found that one DHDDS-like protein acted as a homodimeric cis-PT to make a medium-chain C55 product, while the other formed heterodimeric complexes with either one of two NgBR homologues to produce longer-chain products. Both complexes were functional to complement the growth defect of the yeast rer2 deficient strain at a higher temperature. From the roles for the polyprenol and dolichol biosynthesis and sequence motifs, their homologues in various species were compared to reveal their possible evolutionary paths.
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Affiliation(s)
- Jia‐Jin Liu
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
| | - Po‐Huang Liang
- Institute of Biochemical SciencesNational Taiwan UniversityTaipeiTaiwan
- Institute of Biological ChemistryAcademia SinicaTaipeiTaiwan
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Giladi M, Lisnyansky Bar-El M, Vaňková P, Ferofontov A, Melvin E, Alkaderi S, Kavan D, Redko B, Haimov E, Wiener R, Man P, Haitin Y. Structural basis for long-chain isoprenoid synthesis by cis-prenyltransferases. SCIENCE ADVANCES 2022; 8:eabn1171. [PMID: 35584224 PMCID: PMC9116609 DOI: 10.1126/sciadv.abn1171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
Isoprenoids are synthesized by the prenyltransferase superfamily, which is subdivided according to the product stereoisomerism and length. In short- and medium-chain isoprenoids, product length correlates with active site volume. However, enzymes synthesizing long-chain products and rubber synthases fail to conform to this paradigm, because of an unexpectedly small active site. Here, we focused on the human cis-prenyltransferase complex (hcis-PT), residing at the endoplasmic reticulum membrane and playing a crucial role in protein glycosylation. Crystallographic investigation of hcis-PT along the reaction cycle revealed an outlet for the elongating product. Hydrogen-deuterium exchange mass spectrometry analysis showed that the hydrophobic active site core is flanked by dynamic regions consistent with separate inlet and outlet orifices. Last, using a fluorescence substrate analog, we show that product elongation and membrane association are closely correlated. Together, our results support direct membrane insertion of the elongating isoprenoid during catalysis, uncoupling active site volume from product length.
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Affiliation(s)
- Moshe Giladi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Michal Lisnyansky Bar-El
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Pavla Vaňková
- Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Alisa Ferofontov
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Emelia Melvin
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Suha Alkaderi
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Daniel Kavan
- Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Boris Redko
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Elvira Haimov
- Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, IMRIC, Hadassah Medical School, The Hebrew University, Jerusalem 9112001, Israel
| | - Petr Man
- Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex. Nat Commun 2020; 11:5273. [PMID: 33077723 PMCID: PMC7573591 DOI: 10.1038/s41467-020-18970-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/23/2020] [Indexed: 11/17/2022] Open
Abstract
The human cis-prenyltransferase (hcis-PT) is an enzymatic complex essential for protein N-glycosylation. Synthesizing the precursor of the glycosyl carrier dolichol-phosphate, mutations in hcis-PT cause severe human diseases. Here, we reveal that hcis-PT exhibits a heterotetrameric assembly in solution, consisting of two catalytic dehydrodolichyl diphosphate synthase (DHDDS) and inactive Nogo-B receptor (NgBR) heterodimers. Importantly, the 2.3 Å crystal structure reveals that the tetramer assembles via the DHDDS C-termini as a dimer-of-heterodimers. Moreover, the distal C-terminus of NgBR transverses across the interface with DHDDS, directly participating in active-site formation and the functional coupling between the subunits. Finally, we explored the functional consequences of disease mutations clustered around the active-site, and in combination with molecular dynamics simulations, we propose a mechanism for hcis-PT dysfunction in retinitis pigmentosa. Together, our structure of the hcis-PT complex unveils the dolichol synthesis mechanism and its perturbation in disease. The human cis-prenyltransferase (hcis-PT) complex synthesizes the precursor of the glycosyl carrier dolichol-phosphate and as such it is essential for protein N-glycosylation. The crystal structure of the complex reveals unusual tetrameric architecture and provides insights into dolichol synthesis mechanism and functional consequences of disease-associated hcis-PT mutations.
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Lisnyansky Bar-El M, Lee SY, Ki AY, Kapelushnik N, Loewenstein A, Chung KY, Schneidman-Duhovny D, Giladi M, Newman H, Haitin Y. Structural Characterization of Full-Length Human Dehydrodolichyl Diphosphate Synthase Using an Integrative Computational and Experimental Approach. Biomolecules 2019; 9:E660. [PMID: 31661879 PMCID: PMC6921004 DOI: 10.3390/biom9110660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/25/2019] [Accepted: 10/26/2019] [Indexed: 01/13/2023] Open
Abstract
Dehydrodolichyl diphosphate synthase (DHDDS) is the catalytic subunit of the heteromeric human cis-prenyltransferase complex, synthesizing the glycosyl carrier precursor for N-linked protein glycosylation. Consistent with the important role of N-glycosylation in protein biogenesis, DHDDS mutations result in human diseases. Importantly, DHDDS encompasses a C-terminal region, which does not converge with any known conserved domains. Therefore, despite the clinical importance of DHDDS, our understating of its structure-function relations remains poor. Here, we provide a structural model for the full-length human DHDDS using a multidisciplinary experimental and computational approach. Size-exclusion chromatography multi-angle light scattering revealed that DHDDS forms a monodisperse homodimer in solution. Enzyme kinetics assays revealed that it exhibits catalytic activity, although reduced compared to that reported for the intact heteromeric complex. Our model suggests that the DHDDS C-terminus forms a helix-turn-helix motif, tightly packed against the core catalytic domain. This model is consistent with small-angle X-ray scattering data, indicating that the full-length DHDDS maintains a similar conformation in solution. Moreover, hydrogen-deuterium exchange mass-spectrometry experiments show time-dependent deuterium uptake in the C-terminal domain, consistent with its overall folded state. Finally, we provide a model for the DHDDS-NgBR heterodimer, offering a structural framework for future structural and functional studies of the complex.
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Affiliation(s)
- Michal Lisnyansky Bar-El
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel.
| | - Su Youn Lee
- School of Pharmacy, Sungkyunkwan University, Jangan-gu, Suwon 16419, Korea.
| | - Ah Young Ki
- School of Pharmacy, Sungkyunkwan University, Jangan-gu, Suwon 16419, Korea.
| | - Noa Kapelushnik
- Department of Ophthalmology, Sheba Medical Center, Ramat Gan 5265601, Israel.
| | - Anat Loewenstein
- Department of Ophthalmology, Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Jangan-gu, Suwon 16419, Korea.
| | - Dina Schneidman-Duhovny
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel.
- Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel.
| | - Hadas Newman
- Department of Ophthalmology, Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel.
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel.
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