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Lee J, Sim KM, Kang M, Oh HJ, Choi HJ, Kim YE, Pack CG, Kim K, Kim KM, Oh SH, Kim I, Chang I. Understanding the molecular mechanism of pathogenic variants of BIR2 domain in XIAP-deficient inflammatory bowel disease. Sci Rep 2024; 14:853. [PMID: 38191507 PMCID: PMC10774423 DOI: 10.1038/s41598-023-50932-5] [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: 09/27/2023] [Accepted: 12/28/2023] [Indexed: 01/10/2024] Open
Abstract
X-linked inhibitor of apoptosis protein (XIAP) deficiency causes refractory inflammatory bowel disease. The XIAP protein plays a pivotal role in the pro-inflammatory response through the nucleotide-binding oligomerization domain-containing signaling pathway that is important in mucosal homeostasis. We analyzed the molecular mechanism of non-synonymous pathogenic variants (PVs) of XIAP BIR2 domain. We generated N-terminally green fluorescent protein-tagged XIAP constructs of representative non-synonymous PVs. Co-immunoprecipitation and fluorescence cross-correlation spectroscopy showed that wild-type XIAP and RIP2 preferentially interacted in live cells, whereas all non-synonymous PV XIAPs failed to interact properly with RIP2. Structural analysis showed that various structural changes by mutations, such as hydrophobic core collapse, Zn-finger loss, and spatial rearrangement, destabilized the two loop structures (174-182 and 205-215) that critically interact with RIP2. Subsequently, it caused a failure of RIP2 ubiquitination and loss of protein deficiency by the auto-ubiquitination of all XIAP mutants. These findings could enhance our understanding of the role of XIAP mutations in XIAP-deficient inflammatory bowel disease and may benefit future therapeutic strategies.
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Affiliation(s)
- Juhwan Lee
- iProtein Therapeutics Inc., Munji-ro 281-9, Yuseong-gu, Daejeon, Korea
| | - Kyoung Mi Sim
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Mooseok Kang
- iProtein Therapeutics Inc., Munji-ro 281-9, Yuseong-gu, Daejeon, Korea
| | - Hyun Ju Oh
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Ho Jung Choi
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Yeong Eun Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Chan-Gi Pack
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyunggon Kim
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Mo Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea
| | - Seak Hee Oh
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea.
| | - Inki Kim
- Department of Convergence Medicine, Asan Medical Center, Asan Institutes for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea.
- Department of Pharmacology, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-Gu, Seoul, 05505, Korea.
| | - Iksoo Chang
- Creative Research Initiatives Center for Proteome Biophysics, Department of Brain Sciences and Supercomputing Bigdata Center, DGIST, Daegu, 42988, Korea.
- Department of Brain Sciences and Supercomputing Big Data Center, DGIST, Daegu, 42988, Korea.
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