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Lyophyllin, a Mushroom Protein from the Peptidase M35 Superfamily Is an RNA N-Glycosidase

Ribosome-inactivating proteins (RIPs) hydrolyze the N-glycosidic bond and depurinate a specific adenine residue (A-4324 in rat 28S ribosomal RNA, rRNA) in the conserved α-sarcin/ricin loop (α-SRL) of rRNA. In this study, we have purified and characterized lyophyllin, an unconventional RIP from Lyoph...

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Autores principales: Lu, Jia-Qi, Shi, Wei-Wei, Xiao, Meng-Jie, Tang, Yun-Sang, Zheng, Yong-Tang, Shaw, Pang-Chui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8584072/
https://www.ncbi.nlm.nih.gov/pubmed/34769028
http://dx.doi.org/10.3390/ijms222111598
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author Lu, Jia-Qi
Shi, Wei-Wei
Xiao, Meng-Jie
Tang, Yun-Sang
Zheng, Yong-Tang
Shaw, Pang-Chui
author_facet Lu, Jia-Qi
Shi, Wei-Wei
Xiao, Meng-Jie
Tang, Yun-Sang
Zheng, Yong-Tang
Shaw, Pang-Chui
author_sort Lu, Jia-Qi
collection PubMed
description Ribosome-inactivating proteins (RIPs) hydrolyze the N-glycosidic bond and depurinate a specific adenine residue (A-4324 in rat 28S ribosomal RNA, rRNA) in the conserved α-sarcin/ricin loop (α-SRL) of rRNA. In this study, we have purified and characterized lyophyllin, an unconventional RIP from Lyophyllum shimeji, an edible mushroom. The protein resembles peptidase M35 domain of peptidyl-Lys metalloendopeptidases. Nevertheless, protein either from the mushroom or in recombinant form possessed N-glycosidase and protein synthesis inhibitory activities. A homology model of lyophyllin was constructed. It was found that the zinc binding pocket of this protein resembles the catalytic cleft of a classical RIP, with key amino acids that interact with the adenine substrate in the appropriate positions. Mutational studies showed that E122 may play a role in stabilizing the positively charged oxocarbenium ion and H121 for protonating N-3 of adenine. The tyrosine residues Y137 and Y104 may be used for stacking the target adenine ring. This work first shows a protein in the peptidase M35 superfamily based on conserved domain search possessing N-glycosidase activity.
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spelling pubmed-85840722021-11-12 Lyophyllin, a Mushroom Protein from the Peptidase M35 Superfamily Is an RNA N-Glycosidase Lu, Jia-Qi Shi, Wei-Wei Xiao, Meng-Jie Tang, Yun-Sang Zheng, Yong-Tang Shaw, Pang-Chui Int J Mol Sci Article Ribosome-inactivating proteins (RIPs) hydrolyze the N-glycosidic bond and depurinate a specific adenine residue (A-4324 in rat 28S ribosomal RNA, rRNA) in the conserved α-sarcin/ricin loop (α-SRL) of rRNA. In this study, we have purified and characterized lyophyllin, an unconventional RIP from Lyophyllum shimeji, an edible mushroom. The protein resembles peptidase M35 domain of peptidyl-Lys metalloendopeptidases. Nevertheless, protein either from the mushroom or in recombinant form possessed N-glycosidase and protein synthesis inhibitory activities. A homology model of lyophyllin was constructed. It was found that the zinc binding pocket of this protein resembles the catalytic cleft of a classical RIP, with key amino acids that interact with the adenine substrate in the appropriate positions. Mutational studies showed that E122 may play a role in stabilizing the positively charged oxocarbenium ion and H121 for protonating N-3 of adenine. The tyrosine residues Y137 and Y104 may be used for stacking the target adenine ring. This work first shows a protein in the peptidase M35 superfamily based on conserved domain search possessing N-glycosidase activity. MDPI 2021-10-27 /pmc/articles/PMC8584072/ /pubmed/34769028 http://dx.doi.org/10.3390/ijms222111598 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lu, Jia-Qi
Shi, Wei-Wei
Xiao, Meng-Jie
Tang, Yun-Sang
Zheng, Yong-Tang
Shaw, Pang-Chui
Lyophyllin, a Mushroom Protein from the Peptidase M35 Superfamily Is an RNA N-Glycosidase
title Lyophyllin, a Mushroom Protein from the Peptidase M35 Superfamily Is an RNA N-Glycosidase
title_full Lyophyllin, a Mushroom Protein from the Peptidase M35 Superfamily Is an RNA N-Glycosidase
title_fullStr Lyophyllin, a Mushroom Protein from the Peptidase M35 Superfamily Is an RNA N-Glycosidase
title_full_unstemmed Lyophyllin, a Mushroom Protein from the Peptidase M35 Superfamily Is an RNA N-Glycosidase
title_short Lyophyllin, a Mushroom Protein from the Peptidase M35 Superfamily Is an RNA N-Glycosidase
title_sort lyophyllin, a mushroom protein from the peptidase m35 superfamily is an rna n-glycosidase
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8584072/
https://www.ncbi.nlm.nih.gov/pubmed/34769028
http://dx.doi.org/10.3390/ijms222111598
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