Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants

Gabriel Velez; Young Joo Sun; Saif Khan; Jing Yang; Jonathan Herrmann; Teja Chemudupati; Robert E MacLaren; Lokesh Gakhar; Soichi Wakatsuki; Alexander G Bassuk; Vinit B Mahajan

doi:10.1016/j.celrep.2019.12.077

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Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants

Journal article

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Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants

Gabriel Velez, Young Joo Sun, Saif Khan, Jing Yang, Jonathan Herrmann, Teja Chemudupati, Robert E MacLaren, Lokesh Gakhar, Soichi Wakatsuki, Alexander G Bassuk, …

Cell reports (Cambridge), Vol.30(3), pp.881-892.e5

01/21/2020

DOI: 10.1016/j.celrep.2019.12.077

PMCID: PMC7001764

PMID: 31968260

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Abstract

Increased calpain activity is linked to neuroinflammation including a heritable retinal disease caused by hyper-activating mutations in the calcium-activated calpain-5 (CAPN5) protease. Although structures for classical calpains are known, the structure of CAPN5, a non-classical calpain, remains undetermined. Here we report the 2.8 Å crystal structure of the human CAPN5 protease core (CAPN5-PC). Compared to classical calpains, CAPN5-PC requires high calcium concentrations for maximal activity. Structure-based phylogenetic analysis and multiple sequence alignment reveal that CAPN5-PC contains three elongated flexible loops compared to its classical counterparts. The presence of a disease-causing mutation (c.799G>A, p.Gly267Ser) on the unique PC2L2 loop reveals a function in this region for regulating enzymatic activity. This mechanism could be transferred to distant calpains, using synthetic calpain hybrids, suggesting an evolutionary mechanism for fine-tuning calpain function by modifying flexible loops. Further, the open (inactive) conformation of CAPN5-PC provides structural insight into CAPN5-specific residues that can guide inhibitor design. [Display omitted] •The structure of the human calpain-5 protease core (CAPN5-PC) is determined•CAPN5-PC contains three elongated loops compared to its classical counterparts•One loop contains a mutation identified in a patient with NIV (p.Gly267Ser)•The p.Gly267Ser mutation causes hyperactivity in CAPN5-PC and CAPN1/5-PC hybrids Velez et al. report the crystal structure of the calpain-5 protease core (CAPN5-PC). Sequence- and structure-based phylogenetic analysis reveals that CAPN5-PC contains three elongated loops compared to classical calpains. One loop contains a hyperactivating mutation that causes neovascular inflammatory vitreoretinopathy, revealing a function in this region for regulating proteolytic activity.

protease

disease-causing mutations

calpain

synthetic biology

calcium-binding protein

CAPN5

structural phylogenetics

crystal structure

NIV

uveitis

enzyme kinetics

Details

Title: Subtitle: Structural Insights into the Unique Activation Mechanisms of a Non-classical Calpain and Its Disease-Causing Variants
Creators: Gabriel Velez - Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
Young Joo Sun - Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
Saif Khan - Protein and Crystallography Facility, University of Iowa, Iowa City, IA 52242, USA
Jing Yang - Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
Jonathan Herrmann - Department of Structural Biology, Stanford University, Palo Alto, CA 94305, USA
Teja Chemudupati - Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
Robert E MacLaren - NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford EC1V 2PD, UK
Lokesh Gakhar - Protein and Crystallography Facility, University of Iowa, Iowa City, IA 52242, USA
Soichi Wakatsuki - Department of Structural Biology, Stanford University, Palo Alto, CA 94305, USA
Alexander G Bassuk - Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
Vinit B Mahajan - Omics Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
Resource Type: Journal article
Publication Details: Cell reports (Cambridge), Vol.30(3), pp.881-892.e5
Publisher: Elsevier Inc
DOI: 10.1016/j.celrep.2019.12.077
PMID: 31968260
PMCID: PMC7001764
ISSN: 2211-1247
eISSN: 2211-1247
Grant note: DOI: 10.13039/100000015, name: U.S. Department of Energy; DOI: 10.13039/100000002, name: National Institutes of Health; DOI: 10.13039/100000057, name: National Institute of General Medical Sciences; DOI: 10.13039/100000001, name: National Science Foundation
Language: English
Date published: 01/21/2020
Academic Unit: Neurology; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Biochemistry and Molecular Biology; Neurology (Pediatrics); Medicine Administration
Record Identifier: 9984070990202771

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