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Disruption of CAD Oligomerization by Pathogenic Variants
Open accessPublished version of a preprint
Abstract
ABSTRACT CAD is a multi-enzymatic protein essential for initiating the de novo biosynthesis of pyrimidine nucleotides, forming large hexamers whose structure and function are not fully understood. Defects in CAD result in a severe neurometabolic disorder that is challenging to diagnose. We developed a cellular functional assay to identify defective CAD variants, and in this study, we characterized five pathogenic missense mutations in CAD’s dihydroorotase (DHO) and aspartate transcarbamylase (ATC) domains. All mutations impaired enzymatic activities, with two notably disrupting the formation of DHO dimers and ATC trimers. Combining crystal structures and AlphaFold predictions, we modeled the hexameric CAD complex, highlighting the central role of the DHO and ATC domains in its assembly. Our findings provide insight into CAD’s stability, function, and organization, revealing that correct oligomerization of CAD into a supramolecular complex is required for its function in nucleotide synthesis and that mutations affecting this assembly are potentially pathogenic.
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Cites
UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,828
Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
Matplotlib: a 2D graphics environment
Hunter, J. D. (2007) · Computing in Science & Engineering · doi:10.1109/mcse.2007.55 · Cited by 39,249
Features and development of Coot
Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 29,915
Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015) · SoftwareX · doi:10.1016/j.softx.2015.06.001 · Cited by 27,190
PHENIX : a comprehensive Python-based system for macromolecular structure solution
Adams, P. D., Afonine, P. V., Bunkóczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., et al. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909052925 · Cited by 23,716
Phaser crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612
LINCS: A linear constraint solver for molecular simulations
Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.0.co;2-h · Cited by 18,479
Overview of the CCP 4 suite and current developments
Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910045749 · Cited by 12,353
CHARMM‐GUI: A web‐based graphical user interface for CHARMM
Jo, S., Kim, T., Iyer, V. G., & Im, W. (2008) · Journal of Computational Chemistry · doi:10.1002/jcc.20945 · Cited by 9,284
REFMAC 5 for the refinement of macromolecular crystal structures
Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F., & Vagin, A. A. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444911001314 · Cited by 8,317
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2016) · Nature Methods · doi:10.1038/nmeth.4067 · Cited by 7,334
The FoldX web server: an online force field
Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki387 · Cited by 2,759
Dynamic personalities of proteins
Henzler-Wildman, K., & Kern, D. (2007) · Nature · doi:10.1038/nature06522 · Cited by 2,545
Niesen, F., Berglund, H., & Vedadi, M. (2007) · Nature Protocols · doi:10.1038/nprot.2007.321 · Cited by 2,504
Accurate proteome-wide missense variant effect prediction with AlphaMissense
Cheng, J., Novati, G., Pan, J., Bycroft, C., Žemgulytė, A., Applebaum, T., Pritzel, A., Wong, L. H., Zielinski, M., Sargeant, T., et al. (2023) · Science · doi:10.1126/science.adg7492 · Cited by 2,163
Data processing and analysis with the autoPROC toolbox
Vonrhein, C., Flensburg, C., Keller, P., Sharff, A., Smart, O. S., Paciorek, W. A., Womack, T. O., & Bricogne, G. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444911007773 · Cited by 2,110
Light scattering and the absolute characterization of macromolecules
Wyatt, P. J. (1993) · Analytica Chimica Acta · doi:10.1016/0003-2670(93)80373-s · Cited by 1,436
Stimulation of de novo pyrimidine synthesis by growth signaling through mTOR and S6K1
Ben-Sahra, I., Howell, J. J., Asara, J. M., & Manning, B. D. (2013) · Science · doi:10.1126/science.1228792 · Cited by 739
Pyrimidine Nucleotide Biosynthesis in Animals: Genes, Enzymes, and Regulation of UMP Biosynthesis
Jones, M. E. (1980) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.49.070180.001345 · Cited by 721
Quantitative Phosphoproteomics Reveal mTORC1 Activates de Novo Pyrimidine Synthesis
Robitaille, A. M., Christen, S., Shimobayashi, M., Cornu, M., Fava, L. L., Moes, S., Prescianotto-Baschong, C., Sauer, U., Jenoe, P., & Hall, M. N. (2013) · Science · doi:10.1126/science.1228771 · Cited by 525
Collins, K. D., & Stark, G. R. (1971) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)34156-0 · Cited by 424
Modified methods for the determination of carbamyl aspartate
Prescott, L. M., & Jones, M. E. (1969) · Analytical Biochemistry · doi:10.1016/s0003-2697(69)80008-4 · Cited by 420
IVA cloning: A single-tube universal cloning system exploiting bacterial In Vivo Assembly
García‐Nafría, J., Watson, J. F., & Greger, I. H. (2016) · Scientific Reports · doi:10.1038/srep27459 · Cited by 332
Structure of Carbamoyl Phosphate Synthetase: A Journey of 96 Å from Substrate to Product,
Thoden, J. B., Holden, H. M., Wesenberg, G., Raushel, F. M., & Rayment, I. (1997) · Biochemistry · doi:10.1021/bi970503q · Cited by 302
Coleman, P. F., Suttle, D. P., & Stark, G. R. (1977) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)39968-4 · Cited by 265
Regulation of carbamoyl phosphate synthetase by MAP kinase
Graves, L. M., Guy, H. I., Kozlowski, P., Huang, M., Lazarowski, E. R., Pope, R. M., Collins, M. A., Dahlstrand, E. N., Earp, H. S., & Evans, D. R. (2000) · Nature · doi:10.1038/35002111 · Cited by 241
Additive CHARMM36 Force Field for Nonstandard Amino Acids
Croitoru, A., Park, S., Kumar, A., Lee, J., Im, W., MacKerell, A. D., & Aleksandrov, A. V. (2021) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.1c00254 · Cited by 150
Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF
Monaco, S., Gordon, E. J., Bowler, M. W., Delageniere, S., Guijarro, M., Spruce, D., Svensson, O., McSweeney, S. M., McCarthy, A. A., Leonard, G. A., et al. (2013) · Journal of Applied Crystallography · doi:10.1107/s0021889813006195 · Cited by 135
De novo pyrimidine biosynthetic complexes support cancer cell proliferation and ferroptosis defence
Yang, C., Zhao, Y., Wang, L., Guo, Z., Ma, L., Yang, R., Wu, Y., Li, X., Niu, J., Chu, Q., et al. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01146-4 · Cited by 131
CADmutations and uridine-responsive epileptic encephalopathy
Koch, J., Mayr, J. A., Alhaddad, B., Rauscher, C., Bierau, J., Kovács-Nagy, R., Coene, K. L. M., Bader, I., Holzhacker, M., Prokisch, H., et al. (2016) · Brain · doi:10.1093/brain/aww300 · Cited by 128
Correlating protein function and stability through the analysis of single amino acid substitutions
Bromberg, Y., & Rost, B. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-s8-s8 · Cited by 111
Souciet, J., Nagy, M., Gouar, M. L., Lacroute, F., & Potier, S. (1989) · Gene · doi:10.1016/0378-1119(89)90092-9 · Cited by 101
Ng, B. G., Wolfe, L. A., Ichikawa, M., Markello, T. C., He, M., Tifft, C. J., Gahl, W. A., & Freeze, H. H. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv057 · Cited by 86
de Cima, S., Polo, L. M., Díez‐Fernández, C., Martínez, A. I. E., Cervera, J., Fita, I., & Rubio, V. (2015) · Scientific Reports · doi:10.1038/srep16950 · Cited by 79
Lee, L., Kelly, R. E., Pastra-Landis, S. C., et al. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.20.6802 · Cited by 78
Christopherson, R. I., & Jones, M. (1980) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)70303-2 · Cited by 76
Carrey, E. A., Campbell, D. G., & Hardie, D. G. (1985) · The EMBO Journal · doi:10.1002/j.1460-2075.1985.tb04142.x · Cited by 75
Mally, M. I., Grayson, D. R., & Evans, D. R. (1980) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)70302-0 · Cited by 71
Structure, Functional Characterization, and Evolution of the Dihydroorotase Domain of Human CAD
Grande-García, A., Lallous, N., Díaz-Tejada, C., & Ramón‐Maiques, S. (2013) · Structure · doi:10.1016/j.str.2013.10.016 · Cited by 70
Self-citationDavidson, J. N., Rumsby, P. C., & Tamaren, J. (1981) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)69390-7 · Cited by 68
Moreno‐Morcillo, M., Grande-García, A., Ruiz‐Ramos, A., del Caño‐Ochoa, F., Boskovic, J., & Ramón‐Maiques, S. (2017) · Structure · doi:10.1016/j.str.2017.04.012 · Cited by 62
Self-citationSeifi, M., & Walter, M. A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0195971 · Cited by 48
del Caño‐Ochoa, F., & Ramón‐Maiques, S. (2021) · Protein Science · doi:10.1002/pro.4158 · Cited by 41
Self-citationCAD, A Multienzymatic Protein at the Head of de Novo Pyrimidine Biosynthesis
del Caño‐Ochoa, F., Moreno‐Morcillo, M., & Ramón‐Maiques, S. (2019) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-3-030-28151-9_17 · Cited by 40
Self-citationRuiz‐Ramos, A., Velázquez‐Campoy, A., Grande-García, A., Moreno‐Morcillo, M., & Ramón‐Maiques, S. (2016) · Structure · doi:10.1016/j.str.2016.05.001 · Cited by 39
Self-citationRymen, D., Lindhout, M., Spanou, M., Ashrafzadeh, F., Benkel, I., Betzler, C., Coubes, C., Hartmann, H., Kaplan, J. D., Ballhausen, D., et al. (2020) · Genetics in Medicine · doi:10.1038/s41436-020-0933-z · Cited by 35
Dihydroorotase from Escherichia coli: Loop Movement and Cooperativity between Subunits
Lee, M., Chan, C. W., Guss, J. M., Christopherson, R. I., & Maher, M. J. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.01.067 · Cited by 32
A Patient With CAD Deficiency Responsive to Uridine and Literature Review
Zhou, L., Han, X., Wang, T., & Wu, Y. (2020) · Frontiers in Neurology · doi:10.3389/fneur.2020.00064 · Cited by 29
Cell-based analysis of CAD variants identifies individuals likely to benefit from uridine therapy
del Caño‐Ochoa, F., Ng, B. G., Abedalthagafi, M., Almannai, M., Cohn, R. D., Costain, G., Elpeleg, O. N., Houlden, H., Karimiani, E. G., Liu, P., et al. (2020) · Genetics in Medicine · doi:10.1038/s41436-020-0833-2 · Cited by 27
Self-citationSubstitutions in the aspartate transcarbamoylase domain of hamster CAD disrupt oligomeric structure
Qiu, Y., & Davidson, J. N. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.1.97 · Cited by 23
del Caño‐Ochoa, F., Grande-García, A., Reverte‐López, M., D’Abramo, M., & Ramón‐Maiques, S. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.005494 · Cited by 23
Self-citationLee, M., Maher, M. J., Christopherson, R. I., & Guss, J. M. (2007) · Biochemistry · doi:10.1021/bi701098e · Cited by 21
Triacetyluridine treats epileptic encephalopathy from CAD mutations: a case report and review
Frederick, A. L., Sherer, K., Nguyen, L., Ali, S. A., Garg, A., Haas, R., Sahagian, M., & Bui, J. D. (2020) · Annals of Clinical and Translational Neurology · doi:10.1002/acn3.51257 · Cited by 18
Beyond genetics: Deciphering the impact of missense variants in CAD deficiency
del Caño‐Ochoa, F., Ng, B. G., Rubio‐del‐Campo, A., Mahajan, S., Wilson, M. P., Vilar, M., Rymen, D., Sánchez‐Pintos, P., Kenny, J., Martos, M. L., et al. (2023) · Journal of Inherited Metabolic Disease · doi:10.1002/jimd.12667 · Cited by 18
Self-citationRuiz‐Ramos, A., Lallous, N., Grande-García, A., & Ramón‐Maiques, S. (2013) · Acta Crystallographica Section F Structural Biology and Crystallization Communications · doi:10.1107/s1744309113031114 · Cited by 17
Self-citationUridine‐responsive epileptic encephalopathy due to inherited variants in CAD: A Tale of Two Siblings
McGraw, C. M., Mahida, S., Jayakar, P., et al. (2021) · Annals of Clinical and Translational Neurology · doi:10.1002/acn3.51272 · Cited by 16
OTSUKI, T., Mori, M., & Tatibana, M. (1982) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a134067 · Cited by 15
Russo, R., Marra, R., Andolfo, I., Manna, F., Rosa, G. D., Rosato, B. E., Radhakrishnan, K., Fahey, M. C., & Iolascon, A. (2020) · American Journal of Hematology · doi:10.1002/ajh.25946 · Cited by 14
Lallous, N., Grande-García, A., Molina, R., & Ramón‐Maiques, S. (2012) · Acta Crystallographica Section F Structural Biology and Crystallization Communications · doi:10.1107/s1744309112038857 · Cited by 13
Self-citationQiu, Y., & DAVIDSON, N. J. (1998) · Biochemical Journal · doi:10.1042/bj3290243 · Cited by 9
Recognition of Brain Metastases Using Gadolinium-Enhanced SWI MRI: Proof-of-Concept Study
Ceballos‐Ceballos, J., Loza-Gallardo, D. A., Barajas-Romero, M. A., Cantú-Brito, C. G., & Valdés‐Ferrer, S. I. (2020) · Frontiers in Neurology · doi:10.3389/fneur.2020.00005 · Cited by 8
Yarahmadi, S. G., & Morovvati, S. (2022) · BMC Pediatrics · doi:10.1186/s12887-022-03195-4 · Cited by 8
CAD Deficiency—Another Treatable Early Infantile Epileptic Encephalopathy
Kamate, M., & Patil, S. S. (2020) · Pediatric Neurology · doi:10.1016/j.pediatrneurol.2020.05.001 · Cited by 7
Al‐Otaibi, A., AlAyed, A., Madhi, A. A., Saeed, L. H., Ng, B. G., Freeze, H. H., & Almannai, M. (2021) · Molecular Genetics and Metabolism Reports · doi:10.1016/j.ymgmr.2021.100835 · Cited by 7
A Treatable Genetic Disease Caused by CAD Mutation
Xia, P., Xia, L., Zhang, H., Zhang, J., Yu, S.-Q., Wang, S., Xu, Y., Yao, B., & Ye, J. (2022) · Frontiers in Pediatrics · doi:10.3389/fped.2022.771374 · Cited by 7
Duan, L., Ye, L., Yin, R., Sun, Y., Yu, W., Zhang, Y., Zhong, H., Bao, X., & Tian, X. (2024) · BMC Pediatrics · doi:10.1186/s12887-024-04593-6 · Cited by 7
Whitfield, P. (1995) · Forestry An International Journal of Forest Research · doi:10.1093/forestry/68.1.72-a · Cited by 1
Steinberg‐Shemer, O., Yacobovich, J., Noy‐Lotan, S., Dgany, O., Krasnov, T., Barg, A. A., Landau, Y. E., Kneller, K., Somech, R., Gilad, O., et al. (2023) · British Journal of Haematology · doi:10.1111/bjh.19215 · Cited by 1
Self-citation
Research works printed but not linked: 1
- Darden, 1997, Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems, J. Comput. Chem., 18, 1463
Metadata
- Authors
- Del Caño-Ochoa, F., Ramadane-Morchadi, L., Eixerés, L., Moreno-Morcillo, M., Fernández-Leiro, R., & Ramón-Maiques, S.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- Spanish National Cancer Research Centre (ES)
- Venue
- Journal of Molecular Biology
- Publisher
- Elsevier BV
- Published
- 2024-12
- Volume
- 436
- Issue
- 23
- Pages
- 168832
- ISSN
- 0022-2836 (ISSN-L)
- OpenAlex
- W4403628001
- Cited by
- 2
- References
- 69
- Citations by year
- 2025: 2
- FWCI
- 0.27
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc-nd
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- creativecommons.org/licenses/by-nc-nd/4.0/ (vor)
- Locations
- Journal of Molecular Biology (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (acceptedVersion)
- Funders
- Ramon Areces Foundation
- Spain Ministry of Science and Innovation
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Molecular Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- protein trimerization, protein dimerization, pyrimidine synthesis, neurometabolic disorders
- MeSH terms
- Protein Domains, Aspartate Carbamoyltransferase, Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing), Dihydroorotase, Humans, Models, Molecular, Pentosyltransferases, Protein Conformation, Crystallography, X-Ray, Mutation, Missense, Protein Multimerization
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