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Vijayakrishnan S, Kelly S, Gilbert R, Callow P, Bhella D, Forsyth T, Lindsay J, Byron O. Solution structure and characterisation of the human pyruvate dehydrogenase complex core assembly. J Mol Biol 2010; 399:71-93. [PMID: 20361979 PMCID: PMC2880790 DOI: 10.1016/j.jmb.2010.03.043] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Revised: 03/19/2010] [Accepted: 03/23/2010] [Indexed: 12/02/2022]
Abstract
Mammalian pyruvate dehydrogenase complex (PDC) is a key multi-enzyme assembly that is responsible for glucose homeostasis maintenance and conversion of pyruvate into acetyl-CoA. It comprises a central pentagonal dodecahedral core consisting of two subunit types (E2 and E3BP) to which peripheral enzymes (E1 and E3) bind tightly but non-covalently. Currently, there are two conflicting models of PDC (E2+E3BP) core organisation: the 'addition' model (60+12) and the 'substitution' model (48+12). Here we present the first ever low-resolution structures of human recombinant full-length PDC core (rE2/E3BP), truncated PDC core (tE2/E3BP) and native bovine heart PDC core (bE2/E3BP) obtained by small-angle X-ray scattering and small-angle neutron scattering. These structures, corroborated by negative-stain and cryo electron microscopy data, clearly reveal open pentagonal core faces, favouring the 'substitution' model of core organisation. The native and recombinant core structures are all similar to the truncated bacterial E2 core crystal structure obtained previously. Cryo-electron microscopy reconstructions of rE2/E3BP and rE2/E3BP:E3 directly confirm that the core has open pentagonal faces, agree with scattering-derived models and show density extending outwards from their surfaces, which is much more structurally ordered in the presence of E3. Additionally, analytical ultracentrifugation characterisation of rE2/E3BP, rE2 (full-length recombinant E2-only) and tE2/E3BP supports the substitution model. Superimposition of the small-angle neutron scattering tE2/E3BP and truncated bacterial E2 crystal structures demonstrates conservation of the overall pentagonal dodecahedral morphology, despite evolutionary diversity. In addition, unfolding studies using circular dichroism and tryptophan fluorescence spectroscopy show that the rE2/E3BP is less stable than its rE2 counterpart, indicative of a role for E3BP in core destabilisation. The architectural complexity and lower stability of the E2/E3BP core may be of benefit to mammals, where sophisticated fine-tuning is required for cores with optimal catalytic and regulatory efficiencies.
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Key Words
- pdc, pyruvate dehydrogenase complex
- ogdc, 2-oxoglutarate dehydrogenase complex
- ld, lipoyl domain
- sbd, subunit binding domain
- ctd, c-terminal domain
- pdb, protein data bank
- em, electron microscopy
- auc, analytical ultracentrifugation
- saxs, small-angle x-ray scattering
- sans, small-angle neutron scattering
- sv, sedimentation velocity
- se, sedimentation equilibrium
- gfc, gel-filtration chromatography
- hbm, hydrodynamic bead model
- sas, small-angle scattering
- ctf, contrast transfer function
- edta, ethylenediaminetetraacetic acid
- embl, european molecular biology laboratory
- ill, institut laue langevin
- pyruvate dehydrogenase complex
- sas
- auc
- cryo-em
- gdmcl unfolding
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Affiliation(s)
- S. Vijayakrishnan
- Division of Molecular and Cell Biology, Faculty of Biomedical and Life Sciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK
- Division of Infection and Immunity, Faculty of Biomedical and Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - S.M. Kelly
- Division of Molecular and Cell Biology, Faculty of Biomedical and Life Sciences, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - R.J.C. Gilbert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - P. Callow
- EPSAM and ISTM Research Institutes, Keele University, Staffordshire ST5 5BG, UK
- Partnership for Structural Biology, Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - D. Bhella
- Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
| | - T. Forsyth
- EPSAM and ISTM Research Institutes, Keele University, Staffordshire ST5 5BG, UK
- Partnership for Structural Biology, Institut Laue Langevin, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - J.G. Lindsay
- Division of Molecular and Cell Biology, Faculty of Biomedical and Life Sciences, Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - O. Byron
- Division of Infection and Immunity, Faculty of Biomedical and Life Sciences, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow G12 8TA, UK
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