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Tan M, Peng C, Anderson KA, Chhoy P, Xie Z, Dai L, Park J, Chen Y, Huang H, Zhang Y, Ro J, Wagner GR, Green MF, Madsen AS, Schmiesing J, Peterson BS, Xu G, Ilkayeva OR, Muehlbauer MJ, Braulke T, Mühlhausen C, Backos DS, Olsen CA, McGuire PJ, Pletcher SD, Lombard DB, Hirschey MD, Zhao Y. Lysine glutarylation is a protein posttranslational modification regulated by SIRT5. Cell Metab 2014; 19:605-17. [PMID: 24703693 PMCID: PMC4108075 DOI: 10.1016/j.cmet.2014.03.014] [Citation(s) in RCA: 542] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 11/17/2013] [Accepted: 01/27/2014] [Indexed: 01/20/2023]
Abstract
We report the identification and characterization of a five-carbon protein posttranslational modification (PTM) called lysine glutarylation (Kglu). This protein modification was detected by immunoblot and mass spectrometry (MS), and then comprehensively validated by chemical and biochemical methods. We demonstrated that the previously annotated deacetylase, sirtuin 5 (SIRT5), is a lysine deglutarylase. Proteome-wide analysis identified 683 Kglu sites in 191 proteins and showed that Kglu is highly enriched on metabolic enzymes and mitochondrial proteins. We validated carbamoyl phosphate synthase 1 (CPS1), the rate-limiting enzyme in urea cycle, as a glutarylated protein and demonstrated that CPS1 is targeted by SIRT5 for deglutarylation. We further showed that glutarylation suppresses CPS1 enzymatic activity in cell lines, mice, and a model of glutaric acidemia type I disease, the last of which has elevated glutaric acid and glutaryl-CoA. This study expands the landscape of lysine acyl modifications and increases our understanding of the deacylase SIRT5.
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Affiliation(s)
- Minjia Tan
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Chao Peng
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Kristin A Anderson
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Peter Chhoy
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Zhongyu Xie
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Lunzhi Dai
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Jeongsoon Park
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yue Chen
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - He Huang
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Yi Zhang
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China
| | - Jennifer Ro
- Department of Molecular and Integrative Physiology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gregory R Wagner
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Michelle F Green
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Andreas S Madsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Jessica Schmiesing
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Brett S Peterson
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Guofeng Xu
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Olga R Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Michael J Muehlbauer
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA
| | - Thomas Braulke
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Chris Mühlhausen
- Department of Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Donald S Backos
- Computational Chemistry and Biology Core Facility, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Christian A Olsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Peter J McGuire
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott D Pletcher
- Department of Molecular and Integrative Physiology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - David B Lombard
- Department of Pathology and Institute of Gerontology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew D Hirschey
- Sarah W. Stedman Nutrition and Metabolism Center and Department of Medicine, Duke University Medical Center, Durham, NC 27704, USA.
| | - Yingming Zhao
- The Chemical Proteomics Center and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, People's Republic of China; Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
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Begley DW, Davies DR, Hartley RC, Hewitt SN, Rychel AL, Myler PJ, Van Voorhis WC, Staker BL, Stewart LJ. Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1060-9. [PMID: 21904051 PMCID: PMC3169403 DOI: 10.1107/s1744309111014436] [Citation(s) in RCA: 7] [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: 11/24/2010] [Accepted: 04/17/2011] [Indexed: 11/10/2022]
Abstract
Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.
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Affiliation(s)
- Darren W Begley
- Seattle Structural Genomics Center for Infectious Disease (http://www.ssgcid.org), USA.
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