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Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case.

Aleshin AE, Gramatikova S, Hura GL, Bobkov A, Strongin AY, Stec B, Tainer JA, Liddington RC, Smith JW
Structure 17 1465-75 (2009)
Cited: 20 times
EuropePMC logo PMID: 19913481

Abstract

The M16 family of zinc peptidases comprises a pair of homologous domains that form two halves of a "clam-shell" surrounding the active site. The M16A and M16C subfamilies form one class ("peptidasomes"): they degrade 30-70 residue peptides, and adopt both open and closed conformations. The eukaryotic M16B subfamily forms a second class ("processing proteases"): they adopt a single partly-open conformation that enables them to cleave signal sequences from larger proteins. Here, we report the solution and crystal structures of a prokaryotic M16B peptidase, and demonstrate that it has features of both classes: thus, it forms stable "open" homodimers in solution that resemble the processing proteases; but the clam-shell closes upon binding substrate, a feature of the M16A/C peptidasomes. Moreover, clam-shell closure is required for proteolytic activity. We predict that other prokaryotic M16B family members will form dimeric peptidasomes, and propose a model for the evolution of the M16 family.

Reviews - 3hdi mentioned but not cited (1)

  1. Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation. Márquez-Cantudo L, Ramos A, Coderch C, de Pascual-Teresa B. Molecules 26 5606 (2021)

Articles - 3hdi mentioned but not cited (3)

  1. Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case. Aleshin AE, Gramatikova S, Hura GL, Bobkov A, Strongin AY, Stec B, Tainer JA, Liddington RC, Smith JW. Structure 17 1465-1475 (2009)
  2. Crystal Structure and Function of PqqF Protein in the Pyrroloquinoline Quinone Biosynthetic Pathway. Wei Q, Ran T, Ma C, He J, Xu D, Wang W. J Biol Chem 291 15575-15587 (2016)
  3. Information quantity for secondary structure propensities of protein subsequences in the Protein Data Bank. Kondo R, Kasahara K, Takahashi T. Biophys Physicobiol 19 1-12 (2022)


Reviews citing this publication (1)

  1. Small-angle X-ray and neutron scattering as a tool for structural systems biology. Svergun DI. Biol Chem 391 737-743 (2010)

Articles citing this publication (15)

  1. Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. Classen S, Hura GL, Holton JM, Rambo RP, Rodic I, McGuire PJ, Dyer K, Hammel M, Meigs G, Frankel KA, Tainer JA. J Appl Crystallogr 46 1-13 (2013)
  2. Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme. McCord LA, Liang WG, Dowdell E, Kalas V, Hoey RJ, Koide A, Koide S, Tang WJ. Proc Natl Acad Sci U S A 110 13827-13832 (2013)
  3. The solution configurations of inactive and activated DntR have implications for the sliding dimer mechanism of LysR transcription factors. Lerche M, Dian C, Round A, Lönneborg R, Brzezinski P, Leonard GA. Sci Rep 6 19988 (2016)
  4. Molecular basis of substrate recognition and degradation by human presequence protease. King JV, Liang WG, Scherpelz KP, Schilling AB, Meredith SC, Tang WJ. Structure 22 996-1007 (2014)
  5. Bacterial iron acquisition mediated by outer membrane translocation and cleavage of a host protein. Mosbahi K, Wojnowska M, Albalat A, Walker D. Proc Natl Acad Sci U S A 115 6840-6845 (2018)
  6. Characterization of a Species-Specific Insulinase-Like Protease in Cryptosporidium parvum. Zhang S, Wang Y, Wu H, Li N, Jiang J, Guo Y, Feng Y, Xiao L. Front Microbiol 10 354 (2019)
  7. Thermotolerant genes essential for survival at a critical high temperature in thermotolerant ethanologenic Zymomonas mobilis TISTR 548. Charoensuk K, Sakurada T, Tokiyama A, Murata M, Kosaka T, Thanonkeo P, Yamada M. Biotechnol Biofuels 10 204 (2017)
  8. Heterosubunit composition and crystal structures of a novel bacterial M16B metallopeptidase. Maruyama Y, Chuma A, Mikami B, Hashimoto W, Murata K. J Mol Biol 407 180-192 (2011)
  9. A computational study of the glycine-rich loop of mitochondrial processing peptidase. Kučera T, Otyepka M, Matušková A, Samad A, Kutejová E, Janata J. PLoS One 8 e74518 (2013)
  10. Activity, specificity, and probe design for the smallpox virus protease K7L. Aleshin AE, Drag M, Gombosuren N, Wei G, Mikolajczyk J, Satterthwait AC, Strongin AY, Liddington RC, Salvesen GS. J Biol Chem 287 39470-39479 (2012)
  11. Protease-associated import systems are widespread in Gram-negative bacteria. Grinter R, Leung PM, Wijeyewickrema LC, Littler D, Beckham S, Pike RN, Walker D, Greening C, Lithgow T. PLoS Genet 15 e1008435 (2019)
  12. Helicobacter pylori PqqE is a new virulence factor that cleaves junctional adhesion molecule A and disrupts gastric epithelial integrity. Marques MS, Costa AC, Osório H, Pinto ML, Relvas S, Dinis-Ribeiro M, Carneiro F, Leite M, Figueiredo C. Gut Microbes 13 1-21 (2021)
  13. A conserved rhizobial peptidase that interacts with host-derived symbiotic peptides. Benedict AB, Ghosh P, Scott SM, Griffitts JS. Sci Rep 11 11779 (2021)
  14. Insulinase-like Protease 1 Contributes to Macrogamont Formation in Cryptosporidium parvum. Xu R, Feng Y, Xiao L, Sibley LD. mBio 12 e03405-20 (2021)
  15. Multiple approaches of cellular metabolism define the bacterial ancestry of mitochondria. Geiger O, Sanchez-Flores A, Padilla-Gomez J, Degli Esposti M. Sci Adv 9 eadh0066 (2023)


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