Crystal and Solution Structures of a Prokaryotic M16B Peptidase: an Open and Shut Case

Aleshin, Alexander E.; Gramatikova, Svetlana; Hura, Greg L.; Bobkov, Andrey A.; Strongin, Alex Y.; Stec, Boguslaw; Tainer, John A.; Liddington, Robert; Smith, Jeffrey W.

doi:10.1016/j.str.2009.09.009

Cited by 31 publications

(42 citation statements)

References 37 publications

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“…These data suggest that IDE in solution adopts multiple conformations, including the closed/swinging door, D2/D3 pivot, and D1/D4 pivot states. This is consistent with the dynamic nature of proteins in general and conformational diversity revealed by structures of M16B bacterial protease (16,27) (Fig. S1).…”

Section: Roles Of Ide Swinging Door In Substrate Recognition and Rate Ofsupporting

confidence: 89%

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Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme

McCord¹,

Liang²,

Dowdell

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Insulin-degrading enzyme (IDE) selectively degrades the monomer of amyloidogenic peptides and contributes to clearance of amyloid β (Aβ). Thus, IDE retards the progression of Alzheimer's disease. IDE possesses an enclosed catalytic chamber that engulfs and degrades its peptide substrates; however, the molecular mechanism of IDE function, including substrate access to the chamber and recognition, remains elusive. Here, we captured a unique IDE conformation by using a synthetic antibody fragment as a crystallization chaperone. An unexpected displacement of a door subdomain creates an ∼18-Å opening to the chamber. This swinging-door mechanism permits the entry of short peptides into the catalytic chamber and disrupts the catalytic site within IDE door subdomain. Given the propensity of amyloidogenic peptides to convert into β-strands for their polymerization into amyloid fibrils, they also use such β-strands to stabilize the disrupted catalytic site resided at IDE door subdomain for their degradation by IDE. Thus, action of the swinging door allows IDE to recognize amyloidogenicity by substrate-induced stabilization of the IDE catalytic cleft. Small angle X-ray scattering (SAXS) analysis revealed that IDE exists as a mixture of closed and open states. These open states, which are distinct from the swinging door state, permit entry of larger substrates (e.g., Aβ, insulin) to the chamber and are preferred in solution. Mutational studies confirmed the critical roles of the door subdomain and hinge loop joining the N-and C-terminal halves of IDE for catalysis. Together, our data provide insights into the conformational changes of IDE that govern the selective destruction of amyloidogenic peptides.M16 metalloprotease | X-ray crystallography | substrate recognition P roteins in living organisms face acute and chronic challenges to their integrity, which necessitate proteostatic processes to protect their functions (1). Protein-protease networks play a key role in proteostasis by ensuring proper protein function through protein turnovers (2). Amyloidogenic peptides, such as amyloid β (Aβ) and amylin, present a major challenge to proteostasis, because they can form toxic aggregates that impair diverse physiological functions and contribute to human diseases (3, 4). Insulin-degrading enzyme (IDE), a Zn 2+ -metalloprotease, prefers to degrade amyloidogenic peptides to prevent the formation of amyloid fibrils (3). Exemplary substrates of IDE are insulin and Aβ, which are critical for the development of type 2 diabetes mellitus (DM2) and Alzheimer's disease (AD), respectively. Genetic analyses strongly support functional roles of IDE in the clearance of insulin and Aβ (2, 3). In humans, several single nucleotide polymorphisms at the IDE locus on human chromosome 10q are associated with DM2 and late-onset AD (5, 6).Structural analyses have provided significant insights to substrate recognition and catalysis by IDE. IDE has two ∼50-kDa αβαβα N-terminal (IDE-N) and C-terminal (IDE-C) halves, which are linked by a short hinge loop...

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Section: Roles Of Ide Swinging Door In Substrate Recognition and Rate Ofsupporting

confidence: 89%

“…Crystal structures are available for all three subfamilies: M16A (e.g., IDE and pitrilysin), M16B (e.g., MPP and cytochrome bc1 complex core), and M16C (e.g., PreP and falcilysin) (Fig. S1) (7,13,14,(16)(17)(18)(19). All M16 proteases contain two homologous ∼50-kDa domains, one of which contains a conserved HXXEH zinc ion-binding motif.…”

mentioning

confidence: 99%

Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme

McCord¹,

Liang²,

Dowdell

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…Because of the importance of M16 proteases in the processing and degradation of many essential biological molecules, we need to increase our understanding of their function through structural studies of these enzymes from various sources, including bacteria. 18,19 M16 peptidases are further categorized into three subfamilies (M16A, M16B, and M16C) according to their primary structures. Quaternary structures of M16 members show that enzymes in this family comprise four structurally similar domains.…”

Section: Introductionmentioning

confidence: 99%

“…M16A and M16C peptidases (approximately 100 kDa) contain four domains in a single chain, 9,20 whereas M16B enzymes (approximately 50 kDa) form dimers in which each monomer contains two domains. 6,18 For example, yeast MPP, a well-studied M16B enzyme, functions as a heterodimer consisting of a β subunit containing an HXXEH motif and an α subunit without the motif. 6 The α subunit of the enzyme contains a glycine-rich loop in the Cterminal domain that protrudes into the active site and is essential for catalysis (Fig.…”

Section: Introductionmentioning

confidence: 99%

Heterosubunit Composition and Crystal Structures of a Novel Bacterial M16B Metallopeptidase

Maruyama¹,

Chuma²,

Mikami³

et al. 2011

Journal of Molecular Biology

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“…The H1L/G1L gene products are distantly homologous to the M16 family of bacterial and eukaryotic metallopeptidases (6), which either degrade oligopeptides or truncate the signal peptides from mitochondrion/ chloroplast-secreted proteins (13). The function of poxviral metallopeptidase is poorly understood, but it appears to play a complementary role in virus maturation (8,12,14).…”

mentioning

confidence: 99%

Activity, Specificity, and Probe Design for the Smallpox Virus Protease K7L

Aleshin¹,

Drąg²,

Gombosuren

et al. 2012

Journal of Biological Chemistry

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Background:The K7L protease is required for smallpox virus assembly. Results: K7L requires specific substrate recognition elements, dimerization, and nucleic acid cofactors for maximum activity. Conclusion: We have identified contributors to optimal K7L protease activity and specificity. Significance: This first characterization of a poxvirus processing protease demonstrates the importance of dimerization and extended substrate recognition in the control of activity and specificity.

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Crystal and Solution Structures of a Prokaryotic M16B Peptidase: an Open and Shut Case

Cited by 31 publications

References 37 publications

Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme

Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme

Heterosubunit Composition and Crystal Structures of a Novel Bacterial M16B Metallopeptidase

Activity, Specificity, and Probe Design for the Smallpox Virus Protease K7L

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