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PreprintCited by 13Glycosylation and Glycoproteins ResearchEndoplasmic Reticulum Stress and DiseaseLysosomal Storage Disorders Research

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Peptide: N-Glycanase 1 and Its Relationship with Congenital Disorder of Deglycosylation

Open access
Miao, Xiangguang, Wu, Jin, Chen, Hongping, Lu, Guanting·2022·Nutrients
DOI 10.20944/preprints202203.0148.v1PMC PMC9102325

Preprint — published as 10.3390/nu14091690 · Paper page

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Abstract

The cytosolic PNGase (peptide:N-glycanase; Png1 in yeast; NGLY1/Ngly1 in human/mice), also known as peptide-N4-(N-acetyl-beta-glucosaminyl)-asparagine ami-dase, is a well-conserved deglycosylation enzyme (EC 3.5.1.52) which catalyzes the non-lysosomal hydrolysis of an N(4)-(acetyl-β-D-glucosaminyl) asparagine residue into N-acetyl-β-D-glucosaminylamine and a peptide containing an aspartate residue. This enzyme (NGLY1) plays essential roles in clearance of misfolded or unassembled gly-coproteins through a process named ER-associated degradation (ERAD). Accumulating evidence also points out that NGLY1 deficiency can cause an autosomal recessive hu-man genetic disorder associated with abnormal development and congenital disorder of deglycosylation. In addition, the loss of NGLY1 can affect multiple cellular pathways, including but not limited to NFE2L1 pathway, Creb1/Atf1-AQP pathway, BMP path-way, AMPK pathway, and SLC12A2 ion transporter, which might be the underlying reasons for a constellation of clinical phenotypes of NGLY1 deficiency. The current comprehensive review indeed uncovers the detailed NGLY1’s structure and its im-portant roles for participation in ERAD, involvement in CDDG and potential treatment for NGLY1 deficiency.

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Figures

Figure 1 Brief history of the discovery of PNGase.
Figure 1 Brief history of the discovery of PNGase.CC BY · PubMed Central
Figure 2 Predicted structures for non-animal Ngly1 and the core transglutaminase-like domain. (A) AlphaFold predicted structure of FmeNgly1; (B) AlphaFold predicted structure of SceNgly1; (C) AlphaFold predicted structure of AthNgly1; (D) Sequence alignment of the core transglutaminase-like domain. Fme, Flavobacterium meningosepticum; Sce, Saccharomyces cerevisiae; Ath, Arabidopsis thaliana; Osa, Oryza sativa Japonica; Zma, Zea mays; * represents conserved residuals; red * represents the three residuals of the catalytic triad.
Figure 2 Predicted structures for non-animal Ngly1 and the core transglutaminase-like domain. (A) AlphaFold predicted structure of FmeNgly1; (B) AlphaFold predicted structure of SceNgly1; (C) AlphaFold predicted structure of AthNgly1; (D) Sequence alignment of the core transglutaminase-like domain. Fme, Flavobacterium meningosepticum; Sce, Saccharomyces cerevisiae; Ath, Arabidopsis thaliana; Osa, Oryza sativa Japonica; Zma, Zea mays; * represents conserved residuals; red * represents the three residuals of the catalytic triad.CC BY · PubMed Central
Figure 3 Structural analysis of human NGLY1. (A) Three-dimensional structure predicted by AlphaFold; (B) Intrinsically-disordered region of NGLY1; (C) Alignment of the intrinsically-disordered region; (D) Secondary structure of NGLY1.
Figure 3 Structural analysis of human NGLY1. (A) Three-dimensional structure predicted by AlphaFold; (B) Intrinsically-disordered region of NGLY1; (C) Alignment of the intrinsically-disordered region; (D) Secondary structure of NGLY1.CC BY · PubMed Central
Figure 4 Evolutionary relationships of NGLY1 in 33 taxa. (A) Evolutionary phylogeny; (B) Protein structures of Ngly1.
Figure 4 Evolutionary relationships of NGLY1 in 33 taxa. (A) Evolutionary phylogeny; (B) Protein structures of Ngly1.CC BY · PubMed Central
Figure 5 Glc3Man9GlcNAc2 trimming process and ER-associated degradation pathway (ERAD) involving NGLY1. (A) Glc3Man9GlcNAc2 trimming process; (B) ERAD under normal physiological state; (C) ERAD with NGLY1 deficiency.
Figure 5 Glc3Man9GlcNAc2 trimming process and ER-associated degradation pathway (ERAD) involving NGLY1. (A) Glc3Man9GlcNAc2 trimming process; (B) ERAD under normal physiological state; (C) ERAD with NGLY1 deficiency.CC BY · PubMed Central
Figure 6 Variants of NGLY1 generated by alternative splicing in humans. (A) Transcripts; (B) Protein alignments. Red triangles represent peptide binding sites; Red stars the Cys-His-Asp catalytic triad.
Figure 6 Variants of NGLY1 generated by alternative splicing in humans. (A) Transcripts; (B) Protein alignments. Red triangles represent peptide binding sites; Red stars the Cys-His-Asp catalytic triad.CC BY · PubMed Central
Figure 7 Alternative splicing patterns of NGLY1 in different species.
Figure 7 Alternative splicing patterns of NGLY1 in different species.CC BY · PubMed Central
Figure 8 Protein network involving NLGY1 by STRING.
Figure 8 Protein network involving NLGY1 by STRING.CC BY · PubMed Central
Figure 9 Characterization of mutations of NGLY1. (A) mRNA locations; (B) Amino acid locations; (C) Different types of mutations.
Figure 9 Characterization of mutations of NGLY1. (A) mRNA locations; (B) Amino acid locations; (C) Different types of mutations.CC BY · PubMed Central

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Metadata

Authors
Miao, X., Wu, J., Chen, H., & Lu, G.
Affiliations
  • Nanchang University (CN)
  • Roswell Park Comprehensive Cancer Center (US)
Corresponding author
  • Wu, Jin
  • Chen, Hongping
  • Lu, Guanting
ORCID
Venue
Nutrients
Publisher
MDPI AG
Published
2022-03-10
Volume
14
Issue
9
Pages
1690-1690
ISSN
2072-6643 (ISSN-L)
DOI
10.20944/preprints202203.0148.v1
PMC
PMC9102325
OpenAlex
W4224244065
Cited by
13
References
1
Citations by year
2026: 2 · 2025: 2 · 2024: 6 · 2023: 2 · 2022: 1
FWCI
0.29
Type
journal article
Language
en
Open access
Licence
Locations
  • Nutrients (publishedVersion, cc-by)
  • Preprints.org (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Glycosylation and Glycoproteins Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Endoplasmic Reticulum Stress and Disease
  • Health Sciences › Medicine › Genetics (clinical) › Lysosomal Storage Disorders Research
Keywords
NGLY1, congenital disorders of glycosylation, ER-associated degradation, N-glycosylation, deglycosylation, BMP signaling, AMPK signaling, NKCC1, glycoprotein quality control, protein structure
MeSH terms
Asparagine, Humans, Peptides, Congenital Disorders of Glycosylation, Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase, Solute Carrier Family 12, Member 2

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Miao, X., Wu, J., Chen, H., & Lu, G. (2022). Peptide: N-Glycanase 1 and Its Relationship with Congenital Disorder of Deglycosylation. Nutrients. https://doi.org/10.20944/preprints202203.0148.v1

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