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NGLY1 N-glycanase 1 [ Homo sapiens (human) ]

Gene ID: 55768, updated on 7-Dec-2018

Summary

Official Symbol
NGLY1provided by HGNC
Official Full Name
N-glycanase 1provided by HGNC
Primary source
HGNC:HGNC:17646
See related
Ensembl:ENSG00000151092 MIM:610661
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CDDG; PNG1; CDG1V; PNGase
Summary
This gene encodes an enzyme that catalyzes hydrolysis of an N(4)-(acetyl-beta-D-glucosaminyl) asparagine residue to N-acetyl-beta-D-glucosaminylamine and a peptide containing an aspartate residue. The encoded enzyme may play a role in the proteasome-mediated degradation of misfolded glycoproteins. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Feb 2009]
Expression
Broad expression in testis (RPKM 28.0), lymph node (RPKM 11.3) and 25 other tissues See more
Orthologs

Genomic context

See NGLY1 in Genome Data Viewer
Location:
3p24.2
Exon count:
16
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (25718944..25790039, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (25760435..25831530, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene DNA topoisomerase II beta Neighboring gene microRNA 4442 Neighboring gene cysteine rich protein 1 pseudogene 2 Neighboring gene ribosomal protein L32 pseudogene 11 Neighboring gene TATA-box binding protein associated factor 9b pseudogene 1 Neighboring gene 3-oxoacyl-ACP synthase, mitochondrial Neighboring gene uncharacterized LOC105377000 Neighboring gene long intergenic non-protein coding RNA 692

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of N-glycanase 1 (NGLY1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with N-glycanase 1 (NGLY1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with N-glycanase 1 (NGLY1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystem (from REACTOME)
    N-glycan trimming in the ER and Calnexin/Calreticulin cycle, organism-specific biosystemAfter being synthesized in the ER membrane the 14-sugars lipid-linked oligosaccharide is co-translationally transferred to an unfolded protein, as described in the previous steps. After this point th...
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Protein processing in endoplasmic reticulum, organism-specific biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, organism-specific biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...
  • Protein processing in endoplasmic reticulum, conserved biosystem (from KEGG)
    Protein processing in endoplasmic reticulum, conserved biosystemThe endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylate...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ11005, FLJ12409

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity IGI
Inferred from Genetic Interaction
more info
PubMed 
peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity TAS
Traceable Author Statement
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
glycoprotein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycoprotein catabolic process IDA
Inferred from Direct Assay
more info
PubMed 
protein deglycosylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein deglycosylation IDA
Inferred from Direct Assay
more info
PubMed 
protein deglycosylation IGI
Inferred from Genetic Interaction
more info
PubMed 
protein folding TAS
Traceable Author Statement
more info
 
protein quality control for misfolded or incompletely synthesized proteins IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Names
hPNGase
peptide:N-glycanase
NP_001138765.1
NP_001138766.1
NP_001138767.1
NP_060767.2
XP_005265373.1
XP_005265374.1
XP_011532246.1
XP_016862328.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_034108.1 RefSeqGene

    Range
    5001..76096
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145293.1NP_001138765.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform 2

    See identical proteins and their annotated locations for NP_001138765.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate exon that causes a frameshift and lacks an alternate exon which restores the reading frame, compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
    Source sequence(s)
    AC092798, BC000963, BC007226, BQ017148
    Consensus CDS
    CCDS46778.1
    UniProtKB/Swiss-Prot
    Q96IV0
    Related
    ENSP00000387430.1, ENST00000428257.5
    Conserved Domains (3) summary
    cd10459
    Location:19109
    PUB_PNGase; PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase)
    pfam01841
    Location:275334
    Transglut_core; Transglutaminase-like superfamily
    pfam04721
    Location:439633
    PAW; PNGase C-terminal domain, mannose-binding module PAW
  2. NM_001145294.1NP_001138766.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform 3

    See identical proteins and their annotated locations for NP_001138766.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AK296047, BQ017148, DC329733
    Consensus CDS
    CCDS46777.1
    UniProtKB/Swiss-Prot
    Q96IV0
    Related
    ENSP00000389888.2, ENST00000417874.6
    Conserved Domains (5) summary
    COG1305
    Location:251312
    YebA; Transglutaminase-like enzyme, putative cysteine protease [Posttranslational modification, protein turnover, chaperones]
    pfam01841
    Location:233312
    Transglut_core; Transglutaminase-like superfamily
    pfam03835
    Location:296349
    Rad4; Rad4 transglutaminase-like domain
    pfam04721
    Location:415609
    PAW; PNGase C-terminal domain, mannose-binding module PAW
    cl15262
    Location:167
    PUB; PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins
  3. NM_001145295.1NP_001138767.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an exon in the 3' coding region, which results in a frameshift and an early stop codon compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC092798, BC007226, BC017220, BQ017148
    Consensus CDS
    CCDS46779.1
    UniProtKB/Swiss-Prot
    Q96IV0
    Related
    ENSP00000379886.3, ENST00000396649.7
    Conserved Domains (5) summary
    cd10459
    Location:19109
    PUB_PNGase; PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase)
    COG1305
    Location:293354
    YebA; Transglutaminase-like enzyme, putative cysteine protease [Posttranslational modification, protein turnover, chaperones]
    pfam01841
    Location:275354
    Transglut_core; Transglutaminase-like superfamily
    pfam03835
    Location:338391
    Rad4; Rad4 transglutaminase-like domain
    cl10509
    Location:457538
    PAW; PNGase C-terminal domain, mannose-binding module PAW
  4. NM_018297.4NP_060767.2  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform 1

    See identical proteins and their annotated locations for NP_060767.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC092798, BC007226, BQ017148
    Consensus CDS
    CCDS33719.1
    UniProtKB/Swiss-Prot
    Q96IV0
    Related
    ENSP00000280700.5, ENST00000280700.9
    Conserved Domains (4) summary
    cd10459
    Location:19109
    PUB_PNGase; PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase)
    pfam03835
    Location:338391
    Rad4; Rad4 transglutaminase-like domain
    pfam01841
    Location:275354
    Transglut_core; Transglutaminase-like superfamily
    pfam04721
    Location:457651
    PAW; PNGase C-terminal domain, mannose-binding module PAW

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    25718944..25790039 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005265317.1XP_005265374.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform X4

    Conserved Domains (5) summary
    cd10459
    Location:19109
    PUB_PNGase; PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase)
    COG1305
    Location:293354
    YebA; Transglutaminase-like enzyme, putative cysteine protease [Posttranslational modification, protein turnover, chaperones]
    pfam01841
    Location:275354
    Transglut_core; Transglutaminase-like superfamily
    pfam03835
    Location:338391
    Rad4; Rad4 transglutaminase-like domain
    cl10509
    Location:416483
    PAW; PNGase C-terminal domain, mannose-binding module PAW
  2. XM_005265316.1XP_005265373.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform X1

    Conserved Domains (5) summary
    cd10459
    Location:19109
    PUB_PNGase; PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase)
    COG1305
    Location:293354
    YebA; Transglutaminase-like enzyme, putative cysteine protease [Posttranslational modification, protein turnover, chaperones]
    pfam01841
    Location:275354
    Transglut_core; Transglutaminase-like superfamily
    pfam03835
    Location:338391
    Rad4; Rad4 transglutaminase-like domain
    pfam04721
    Location:416596
    PAW; PNGase C-terminal domain, mannose-binding module PAW
  3. XM_011533944.1XP_011532246.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform X3

    See identical proteins and their annotated locations for XP_011532246.1

    Conserved Domains (5) summary
    COG1305
    Location:216277
    YebA; Transglutaminase-like enzyme, putative cysteine protease [Posttranslational modification, protein turnover, chaperones]
    pfam01841
    Location:198277
    Transglut_core; Transglutaminase-like superfamily
    pfam03835
    Location:261314
    Rad4; Rad4 transglutaminase-like domain
    pfam04721
    Location:380574
    PAW; PNGase C-terminal domain, mannose-binding module PAW
    cl15262
    Location:132
    PUB; PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins
  4. XM_017006839.2XP_016862328.1  peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase isoform X2

RNA

  1. XR_001740200.2 RNA Sequence

  2. XR_002959548.1 RNA Sequence

  3. XR_940471.2 RNA Sequence

    Related
    ENST00000280699.13

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_025105.1: Suppressed sequence

    Description
    NM_025105.1: This RefSeq was permanently suppressed because it is primarily intronic sequence.
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