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Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms.

Hori T, Kumasaka T, Yamamoto M, Nonaka N, Tanaka N, Hashimoto Y, Ueki U, Takio K
Acta Crystallogr D Biol Crystallogr 57 361-8 (2001)
Related entries: 1g12, 1ge5, 1ge6

Cited: 24 times
EuropePMC logo PMID: 11223512

Abstract

Crystal structures of a peptidyl-Lys metalloendopeptidase (MEP) from the edible mushroom Grifola frondosa (GfMEP) were solved in four crystal forms. This represents the first structure of the new family 'aspzincins' with a novel active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs conserved among aspzincins. His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner. A Tyr133 side chain located on the S1' pocket had different configurations in two crystal forms and was not observed in the other crystal forms. The flexible Tyr133 plays two roles in the enzymatic function of GfMEP. The first is to provide a hydrophobic environment with Phe83 in order to accommodate the alkyl part of the Lys side chain of a substrate and the second is as a 'proton donor' to the oxyanion of the tetrahedral transition state to stabilize the reaction transition state.

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  1. Structural aspects of the metzincin clan of metalloendopeptidases. Gomis-Rüth FX. Mol Biotechnol 24 157-202 (2003)
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  2. Independent expansion of zincin metalloproteinases in Onygenales fungi may be associated with their pathogenicity. Li J, Zhang KQ. PLoS One 9 e90225 (2014)
  3. Mutational analysis of the catalytic centre of the Citrobacter freundii AmpD N-acetylmuramyl-L-alanine amidase. Généreux C, Dehareng D, Devreese B, Van Beeumen J, Frère JM, Joris B. Biochem J 377 111-120 (2004)
  4. A method for N-terminal de novo sequence analysis of proteins by matrix-assisted laser desorption/ionization mass spectrometry. Kuyama H, Sonomura K, Nishimura O, Tsunasawa S. Anal Biochem 380 291-296 (2008)
  5. Cloning and developmental expression of a metzincin family metalloprotease cDNA from oyster mushroom Pleurotus ostreatus. Joh JH, Kim BG, Kong WS, Yoo YB, Kim NK, Park HR, Cho BG, Lee CS. FEMS Microbiol Lett 239 57-62 (2004)
  6. Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N. Hohmann L, Sherwood C, Eastham A, Peterson A, Eng JK, Eddes JS, Shteynberg D, Martin DB. J Proteome Res 8 1415-1422 (2009)
  7. A method for the isolation of blocked N-terminal peptides. Coussot G, Hawke DH, Mularz A, Koomen JM, Kobayashi R. Anal Biochem 361 302-304 (2007)
  8. The AsaP1 peptidase of Aeromonas salmonicida subsp. achromogenes is a highly conserved deuterolysin metalloprotease (family M35) and a major virulence factor. Arnadottir H, Hvanndal I, Andresdottir V, Burr SE, Frey J, Gudmundsdottir BK. J Bacteriol 191 403-410 (2009)
  9. A method for N-terminal de novo sequencing of Nα-blocked proteins by mass spectrometry. Nakajima C, Kuyama H, Nakazawa T, Nishimura O, Tsunasawa S. Analyst 136 113-119 (2011)
  10. Molecular evolution of the deuterolysin (M35) family genes in Coccidioides. Li J, Yu L, Tian Y, Zhang KQ. PLoS One 7 e31536 (2012)
  11. Esterolytic antibodies as mechanistic and structural models of hydrolases-a quantitative analysis. Lindner AB, Kim SH, Schindler DG, Eshhar Z, Tawfik DS. J Mol Biol 320 559-572 (2002)
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  13. Tryp-N: A Thermostable Protease for the Production of N-terminal Argininyl and Lysinyl Peptides. Wilson JP, Ipsaro JJ, Del Giudice SN, Turna NS, Gauss CM, Dusenbury KH, Marquart K, Rivera KD, Pappin DJ. J Proteome Res 19 1459-1469 (2020)
  14. Efficient Entropy-Driven Inhibition of Dipeptidyl Peptidase III by Hydroxyethylene Transition-State Peptidomimetics. Ivkovic J, Jha S, Lembacher-Fadum C, Puschnig J, Kumar P, Reithofer V, Gruber K, Macheroux P, Breinbauer R. Chemistry 27 14108-14120 (2021)
  15. Genome-Wide Identification of M35 Family Metalloproteases in Rhizoctonia cerealis and Functional Analysis of RcMEP2 as a Virulence Factor during the Fungal Infection to Wheat. Pan L, Wen S, Yu J, Lu L, Zhu X, Zhang Z. Int J Mol Sci 21 E2984 (2020)
  16. PCR cloning and heterologous expression of cDNA encoding a peptidyl-Lys metalloendopeptidase precursor of Grifola frondosa. Saito T, Dohmae N, Tsujimoto M, Takio K. J Gen Appl Microbiol 48 287-292 (2002)
  17. Letter Structural evidence of intramolecular propeptide inhibition of the aspzincin metalloendopeptidase AsaP1. Bogdanović X, Palm GJ, Schwenteit J, Singh RK, Gudmundsdóttir BK, Hinrichs W. FEBS Lett 590 3280-3294 (2016)
  18. Toxoid construction of AsaP1, a lethal toxic aspzincin metalloendopeptidase of Aeromonas salmonicida subsp. achromogenes, and studies of its activity and processing. Schwenteit J, Bogdanović X, Fridjonsson OH, Aevarsson A, Bornscheuer UT, Hinrichs W, Gudmundsdottir BK. Vet Microbiol 162 687-694 (2013)
  19. Heterologous expression of peptidyl-Lys metallopeptidase of Armillaria mellea and mutagenic analysis of the recombinant peptidase. Ødum AS, Østergaard S, Nørby I, Meldal M, Olesen K. J Biochem 159 461-470 (2016)


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