Mutational spectrum of D-bifunctional protein deficiency and structure-based genotype–phenotype analysis
Open accessAbstract
D-bifunctional protein (DBP) deficiency is an autosomal recessive inborn error of peroxisomal fatty acid oxidation. The clinical presentation of DBP deficiency is usually very severe, but a few patients with a relatively mild presentation have been identified. In this article, we report the mutational spectrum of DBP deficiency on the basis of molecular analysis in 110 patients. We identified 61 different mutations by DBP cDNA analysis, 48 of which have not been reported previously. The predicted effects of the different disease-causing amino acid changes on protein structure were determined using the crystal structures of the (3R)-hydroxyacyl-coenzyme A (CoA) dehydrogenase unit of rat DBP and the 2-enoyl-CoA hydratase 2 unit and liganded sterol carrier protein 2-like unit of human DBP. The effects ranged from the replacement of catalytic amino acid residues or residues in direct contact with the substrate or cofactor to disturbances of protein folding or dimerization of the subunits. To study whether there is a genotype-phenotype correlation for DBP deficiency, these structure-based analyses were combined with extensive biochemical analyses of patient material (cultured skin fibroblasts and plasma) and available clinical information on the patients. We found that the effect of the mutations identified in patients with a relatively mild clinical and biochemical presentation was less detrimental to the protein structure than the effect of mutations identified in those with a very severe presentation. These results suggest that the amount of residual DBP activity correlates with the severity of the phenotype. From our data, we conclude that, on the basis of the predicted effect of the mutations on protein structure, a genotype-phenotype correlation exists for DBP deficiency.
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The severe form of DBP deficiency mimics Zellweger syndrome in all aspects including cranio-facial dysmorphism, neuronal migration defects and premature death.
“The severe form of DBP deficiency mimics Zellweger syndrome in all aspects including cranio-facial dysmorphism, neuronal migration defects (similar to that depicted in Fig. 2A) and premature death [84].”
From Peroxisomes in brain development and function (2016) · cites this paper as [84]
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Cites
Berman, H. M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.235 · Cited by 40,196 · see citing works
Jones, T. A., Zou, J.-Y., Cowan, S. W., & Kjeldgaard, M. (1991) · Acta Crystallographica Section A Foundations of Crystallography · doi:10.1107/s0108767390010224 · Cited by 12,650 · see citing works
SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling
Guex, N., & Peitsch, M. (1997) · Electrophoresis · doi:10.1002/elps.1150181505 · Cited by 11,589 · see citing works
Critical Residues for Structure and Catalysis in Short-chain Dehydrogenases/Reductases
Filling, C., Berndt, K. D., Benach, J., Knapp, S., Prozorovski, T., Nordling, E., Ladenstein, R., Jörnvall, H., & Oppermann, U. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m202160200 · Cited by 583 · see citing works
Leesong, M., Henderson, B. S., Gillig, J. R., Schwab, J. M., & Smith, J. L. (1996) · Structure · doi:10.1016/s0969-2126(96)00030-5 · Cited by 276 · see citing works
Adamski, J., Normand, T., Leenders, F., Monté, D., Begue, A., Stéhelin, D., Jungblut, P. W., & de Launoit, Y. (1995) · Biochemical Journal · doi:10.1042/bj3110437 · Cited by 214 · see citing works
van Grunsven, E. G., van Berkel, E., Ijlst, L., Vreken, P., de Klerk, J. B. C., Adamski, J., Lemonde, H., Clayton, P. T., Cuebas, D. A., & Wanders, R. J. A. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.5.2128 · Cited by 152 · see citing works
Self-citationvan Grunsven, E. G., van Berkel, E., Mooijer, P. A. W., Watkins, P. A., Moser, H. W., Suzuki, Y., Jiang, L., Hashimoto, T., Höefler, G., Adamski, J., et al. (1999) · The American Journal of Human Genetics · doi:10.1086/302180 · Cited by 108 · see citing works
Self-citationSuzuki, Y., Jiang, L., Souri, M., Miyazawa, S., Fukuda, S., Zhang, Z., Une, M., Shimozawa, N., Kondo, N., Orii, T., et al. (1997) · The American Journal of Human Genetics · doi:10.1086/301599 · Cited by 107 · see citing works
Vreken, P., van Lint, A. E. M., Bootsma, A. H., Overmars, H., Wanders, R. J. A., & Gennip, A. H. (1998) · Journal of Chromatography B Biomedical Sciences and Applications · doi:10.1016/s0378-4347(98)00186-8 · Cited by 99 · see citing works
Self-citationMeasurement of peroxisomal fatty acid β‐oxidation in cultured human skin fibroblasts
Wanders, R. J. A., Denis, S. W., Ruiter, J. P. N., Schutgens, R. B. H., van Roermund, C. W. T., & Jacobs, B. S. (1995) · Journal of Inherited Metabolic Disease · doi:10.1007/bf00711434 · Cited by 95 · see citing works
Self-citationJiang, L., Kurosawa, T., Sato, M., Suzuki, Y., & Hashimoto, T. (1997) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a021615 · Cited by 86 · see citing works
Bootsma, A. H., Overmars, H., van Rooij, A., et al. (1999) · Journal of Inherited Metabolic Disease · doi:10.1023/a:1005543802724 · Cited by 84 · see citing works
Haapalainen, A. M., van Aalten, D. M. F., Meriläinen, G., Jalonen, J. E., Pirilä, P., Wierenga, R. K., Hiltunen, J. K., & Glumoff, T. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.5084 · Cited by 74 · see citing works
Self-citationJiang, L., Kobayashi, A., Matsuura, H., et al. (1996) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a021458 · Cited by 73 · see citing works
A Two-domain Structure of One Subunit Explains Unique Features of Eukaryotic Hydratase 2
Koski, M. K., Haapalainen, A. M., Hiltunen, J. K., & Glumoff, T. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m400293200 · Cited by 68 · see citing works
Self-citationStudies on phytanic acid α-oxidation in rat liver and cultured human skin fibroblasts
Wanders, R. J. A., & van Roermund, C. W. T. (1993) · Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism · doi:10.1016/0005-2760(93)90239-6 · Cited by 57 · see citing works
Self-citationLeenders, F., Husen, B., Thole, H. H., & Adamski, J. (1994) · Molecular and Cellular Endocrinology · doi:10.1016/0303-7207(94)90114-7 · Cited by 57 · see citing works
Dieuaide‐Noubhani, M., Asselberghs, S., Mannaerts, G. P., & Veldhoven, P. P. V. (1997) · Biochemical Journal · doi:10.1042/bj3250367 · Cited by 57 · see citing works
Enoyl-CoA Hydratase Deficiency: Identification of a New Type of D-Bifunctional Protein Deficiency
van Grunsven, E. G., Mooijer, P. A. W., Aubourg, P. R., & Wanders, R. J. A. (1999) · Human Molecular Genetics · doi:10.1093/hmg/8.8.1509 · Cited by 55 · see citing works
Self-citationCrystal Structure of 2-Enoyl-CoA Hydratase 2 from Human Peroxisomal Multifunctional Enzyme Type 2
Koski, M. K., Haapalainen, A. M., Hiltunen, J. K., & Glumoff, T. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.11.009 · Cited by 54 · see citing works
Self-citationHuman Peroxisomal Multifunctional Enzyme Type 2
Qin, Y.-M., Haapalainen, A. M., Kilpeläinen, S. H., Marttila, M. S., Koski, M. K., Glumoff, T., Novikov, D. K., & Hiltunen, J. K. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.7.4965 · Cited by 51 · see citing works
Self-citationFerdinandusse, S., van Grunsven, E. G., Oostheim, W., Denis, S. W., Hogenhout, E. M., IJlst, L., van Roermund, C. W. T., Waterham, H. R., Goldfischer, S. L., & Wanders, R. J. A. (2002) · The American Journal of Human Genetics · doi:10.1086/340970 · Cited by 48 · see citing works
Self-citationQin, Y.-M., Haapalainen, M., Conry, D. W., CUEBAS, A. D., Hiltunen, J. K., & Novikov, K. (1997) · Biochemical Journal · doi:10.1042/bj3280377 · Cited by 46 · see citing works
Self-citationNovikov, D., Dieuaide‐Noubhani, M., Vermeesch, J. R., Fournier, B., Mannaerts, G. P., & Veldhoven, P. P. V. (1997) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/s0925-4439(97)00003-3 · Cited by 44 · see citing works
Structure of D-3-Hydroxyacyl-CoA Dehydratase/D-3-Hydroxyacyl-CoA Dehydrogenase Bifunctional Protein
Jiang, L., Miyazawa, S., Souri, M., & Hashimoto, T. (1997) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a021596 · Cited by 44 · see citing works
Qin, Y.-M., Marttila, M. S., Haapalainen, A. M., Siivari, K. M., Glumoff, T., & Hiltunen, J. K. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.40.28619 · Cited by 41 · see citing works
Self-citationMalila, L. H., Siivari, K. M., Mäkelä, M., Jalonen, J. E., Latipää, P. M., Kunau, W. H., & Hiltunen, J. K. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(20)80580-8 · Cited by 34 · see citing works
Self-citationPaton, B. C., Sharp, P. C., Crane, D. I., & Poulos, A. (1996) · Journal of Clinical Investigation · doi:10.1172/jci118465 · Cited by 30 · see citing works
Haapalainen, A. M., Koski, M. K., Qin, Y.-M., Hiltunen, J. K., & Glumoff, T. (2003) · Structure · doi:10.1016/s0969-2126(02)00931-0 · Cited by 27 · see citing works
Self-citationItoh, M., Suzuki, Y., Akaboshi, S., et al. (2000) · Brain Research · doi:10.1016/s0006-8993(99)02423-3 · Cited by 25 · see citing works
Paton, B. C., & Pollard, A. N. (2000) · Cell Biochemistry and Biophysics · doi:10.1385/cbb:32:1-3:247 · Cited by 20 · see citing works
Gloerich, J., Denis, S. W., van Grunsven, E. G., Dacremont, G., Wanders, R. J. A., & Ferdinandusse, S. (2003) · Journal of Lipid Research · doi:10.1194/jlr.d200039-jlr200 · Cited by 16 · see citing works
Self-citationNew 17β‐Hydroxysteroid Dehydrogenases
Adamski, J., Carstensen, J. F., Husen, B., KAUFMANN, M., de Launoit, Y., Leenders, F., Markus, M., & Jungblut, P. W. (1996) · Annals of the New York Academy of Sciences · doi:10.1111/j.1749-6632.1996.tb16232.x · Cited by 13 · see citing works
Schr�der, J. M., Hackel, V., Wanders, R. J. A., et al. (2004) · Acta Neuropathologica · doi:10.1007/s00401-004-0877-4 · Cited by 12 · see citing works
Self-citationPaton, B. C., Solly, P. B., Nelson, P. V., Pollard, A. N., Sharp, P. C., & Fietz, M. (2002) · Prenatal Diagnosis · doi:10.1002/pd.233 · Cited by 7 · see citing works
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Peroxisomes in brain development and function
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Lines, M. A., Jobling, R., Brady, L., Marshall, C. R., Scherer, S. W., Rodriguez, A. R., Lee, L., Lang, A. E., Mestre, T. A., Wanders, R. J. A., et al. (2014) · Neurology · doi:10.1212/wnl.0000000000000219 · Cited by 70 · see citing works
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- Authors
- Ferdinandusse, S., Ylianttila, M. S., Gloerich, J., Koski, M. K., Oostheim, W., Waterham, H. R., Hiltunen, J. K., Wanders, R. J. A., & Glumoff, T.
- Affiliations
- Amsterdam UMC Location University of Amsterdam (NL)
- University of Oulu (FI)
- Corresponding author
- Ferdinandusse, Sacha
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2006-01
- Volume
- 78
- Issue
- 1
- Pages
- 112-124
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC1380208
- OpenAlex
- W1995426334
- Cited by
- 96
- References
- 36
- Citations by year
- 2026: 6 · 2025: 4 · 2024: 4 · 2023: 7 · 2022: 4 · 2021: 6 · 2020: 5 · 2019: 3 · 2018: 4 · 2017: 5 · 2016: 5 · 2015: 6 · 2014: 5 · 2013: 7 · 2012: 6
- FWCI
- 1.79
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Pure Amsterdam UMC (submittedVersion)
- Funders
- European Commission
- Academy of Finland
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (916.46.109, 910.31.604)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Metabolism and Genetic Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and rare skin diseases.
- Keywords
- D-bifunctional protein deficiency, DBP, mutation spectrum, peroxisomal fatty acid oxidation, genotype-phenotype correlation, protein structure, sterol carrier protein 2, residual enzyme activity, disease severity
- MeSH terms
- Long-Chain-Fatty-Acid-CoA Ligase, Amino Acid Sequence, Base Sequence, Coenzyme A Ligases, DNA Mutational Analysis, Enoyl-CoA Hydratase, Fatty Acids, Fibroblasts, Fluorescent Antibody Technique, Genotype, Humans, Hydro-Lyases, Models, Molecular, Molecular Sequence Data, Multienzyme Complexes, Mutation, Phenotype, 17-Hydroxysteroid Dehydrogenases, Immunoblotting, Sequence Analysis, DNA, Protein Folding, DNA Primers, Dimerization, Peroxisomal Multifunctional Protein-2
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