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Neprosin belongs to a new family of glutamic peptidase based on in silico evidence
Open accessPublished version of a preprint
Abstract
Neprosin was first discovered in the insectivorous tropical pitcher plants of Nepenthes species as a novel protease with prolyl endopeptidase (PEP) activity. Neprosin has two uncharacterized domains of neprosin activation peptide and neprosin. A previous study has shown neprosin activity in hydrolyzing proline-rich gliadin, a gluten component that triggers celiac disease. In this study, we performed in silico structure-function analysis to investigate the catalytic mechanism of neprosin. Neprosin sequences lack the catalytic triad and motifs of PEP family S9. Protein structures of neprosins from Nepenthes × ventrata (NvNpr) and N. rafflesiana (NrNpr1) were generated by ab initio methods and comparatively assessed to obtain high-quality models. Structural alignment of models to experimental structures in the Protein Data Bank (PDB) found a high structural similarity to glutamic peptidases. Further investigations reveal other resemblances to the glutamic peptidases with low optimum pH that activates the enzyme via autoproteolysis for maturation. Two highly conserved glutamic acid residues, which are stable according to the molecular dynamics simulation, can be found at the active site of the substrate cleft. Protein docking demonstrated that mature neprosins bind well with potent antigen αI-gliadin at the putative active site. Taken together, neprosins represent a new glutamic peptidase family, with a putative catalytic dyad of two glutamic acids. This study illustrates a hypothetical enzymatic mechanism of the neprosin family and demonstrates the useful application of an accurate ab initio protein structure prediction in the structure-function study of a novel protein family.
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Metadata
- Authors
- Ting, T.-Y., Baharin, A., Ramzi, A. B., Ng, C.-L., & Goh, H.-H.
- Affiliations
- National University of Malaysia (MY)
- Corresponding author
- Goh, Hoe-Han
- Venue
- Plant Physiology and Biochemistry
- Publisher
- Elsevier BV
- Published
- 2022-07
- Volume
- 183
- Pages
- 23-35
- ISSN
- 0981-9428 (ISSN-L)
- OpenAlex
- W4225261257
- Cited by
- 17
- References
- 58
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 4 · 2023: 3 · 2022: 5
- FWCI
- 1.23
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- cc-by-nc-nd
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Plant Physiology and Biochemistry (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Universiti Kebangsaan Malaysia (DIP-2020-005)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Protease and Inhibitor Mechanisms
- Keywords
- prolyl endopeptidase, Nepenthes, pitcher plants, celiac disease, catalytic dyad, glutamate residues, autoproteolysis, ab initio protein structure prediction, structure-function analysis, enzyme mechanism
- MeSH terms
- Gliadin, Peptide Hydrolases, Peptides, Catalytic Domain, Proteolysis
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- The paper
- Ting, T.-Y., Baharin, A., Ramzi, A. B., Ng, C.-L., & Goh, H.-H. (2022). Neprosin belongs to a new family of glutamic peptidase based on in silico evidence. Plant Physiology and Biochemistry. https://doi.org/10.1016/j.plaphy.2022.04.027
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