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Protein

Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase

Gene

PNG1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Specifically deglycosylates the denatured form of N-linked glycoproteins in the cytoplasm and assists their proteasome-mediated degradation. Cleaves the beta-aspartyl-glucosamine (GlcNAc) of the glycan and the amide side chain of Asn, converting Asn to Asp. Prefers proteins containing high-mannose over those bearing complex type oligosaccharides. Can recognize misfolded proteins in the endoplasmic reticulum that are exported to the cytosol to be destroyed and deglycosylate them, while it has no activity toward native proteins. Deglycosylation is a prerequisite for subsequent proteasome-mediated degradation of some, but not all, misfolded glycoproteins. Involved in the formation of free oligosaccharide in cytosol.6 Publications

Catalytic activityi

Hydrolysis of an N(4)-(acetyl-beta-D-glucosaminyl)asparagine residue in which the glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D-glucosaminylamine and a peptide containing an aspartate residue.

Cofactori

Zn2+1 PublicationNote: Binds 1 zinc ion per subunit.1 Publication

Enzyme regulationi

Inhibited by Z-VAD-fmk, a well-known caspase inhibitor. Also inhibited by Man9GlcNAc2-iodoacetoamide. Both molecules inhibit enzyme activity through covalent binding of the carbohydrate to the single Cys-191 residue.3 Publications

Kineticsi

  1. KM=210 µM for asialofetuin1 Publication
  1. Vmax=140 nmol/min/mg enzyme with asialofetuin as substrate1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi129 – 1291Zinc
Metal bindingi132 – 1321Zinc
Metal bindingi165 – 1651Zinc
Metal bindingi168 – 1681Zinc
Active sitei191 – 1911Nucleophile
Active sitei218 – 2181
Active sitei235 – 2351
Binding sitei238 – 2381Substrate

GO - Molecular functioni

GO - Biological processi

  • misfolded or incompletely synthesized protein catabolic process Source: SGD
  • protein deglycosylation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:YPL096W-MONOMER.
BRENDAi3.5.1.52. 984.

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase (EC:3.5.1.52)
Short name:
PNGase
Alternative name(s):
Peptide:N-glycanase 1
Short name:
yPNG1
Gene namesi
Name:PNG1
Ordered Locus Names:YPL096W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XVI

Organism-specific databases

EuPathDBiFungiDB:YPL096W.
SGDiS000006017. PNG1.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: SGD
  • nucleus Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi123 – 1231W → A: No effect. 1 Publication
Mutagenesisi129 – 1291C → A or S: Abolishes enzyme activity. 1 Publication
Mutagenesisi132 – 1321C → A or S: Abolishes enzyme activity. 1 Publication
Mutagenesisi165 – 1651C → A or S: Abolishes enzyme activity. 1 Publication
Mutagenesisi168 – 1681C → A or S: Abolishes enzyme activity. 1 Publication
Mutagenesisi174 – 1741F → A: No effect. 1 Publication
Mutagenesisi177 – 1771Y → A: No effect. 1 Publication
Mutagenesisi187 – 1871R → A: No effect. 1 Publication
Mutagenesisi189 – 1891G → A: No effect. 1 Publication
Mutagenesisi191 – 1911C → A: Abolishes enzyme activity. 1 Publication
Mutagenesisi194 – 1941W → A: No effect. 1 Publication
Mutagenesisi198 – 1981F → A: No effect. 1 Publication
Mutagenesisi199 – 1991T → A: No effect. 1 Publication
Mutagenesisi203 – 2031K → A: No effect. 1 Publication
Mutagenesisi206 – 2061G → A: No effect. 1 Publication
Mutagenesisi210 – 2101R → A: Abolishes enzyme activity. 1 Publication
Mutagenesisi212 – 2121V → A: No effect. 1 Publication
Mutagenesisi218 – 2181H → A: Abolishes enzyme activity. 2 Publications
Mutagenesisi218 – 2181H → Y in png1-1; abolishes enzyme activity. 2 Publications
Mutagenesisi220 – 2201W → A: Abolishes enzyme activity. 1 Publication
Mutagenesisi220 – 2201W → F: No effect. 1 Publication
Mutagenesisi222 – 2221E → A: Abolishes enzyme activity. 1 Publication
Mutagenesisi224 – 2241F → A: No effect. 1 Publication
Mutagenesisi230 – 2301R → A: No effect. 1 Publication
Mutagenesisi231 – 2311W → A: Abolishes enzyme activity.
Mutagenesisi231 – 2311W → F: No effect.
Mutagenesisi234 – 2341V → A: No effect. 1 Publication
Mutagenesisi235 – 2351D → A: Abolishes enzyme activity. 1 Publication
Mutagenesisi242 – 2421D → A: No effect. 1 Publication
Mutagenesisi251 – 2511W → A: No effect. 1 Publication
Mutagenesisi253 – 2531K → A: No effect. 1 Publication
Mutagenesisi257 – 2571Y → A: Abolishes enzyme activity. 1 Publication
Mutagenesisi261 – 2611F → A: Abolishes enzyme activity. 1 Publication
Mutagenesisi264 – 2641D → A: No effect. 1 Publication
Mutagenesisi266 – 2661V → A: No effect. 1 Publication
Mutagenesisi268 – 2681D → A: Abolishes enzyme activity. 1 Publication
Mutagenesisi273 – 2731Y → A: Abolishes enzyme activity. 1 Publication
Mutagenesisi281 – 2811R → A: No effect. 1 Publication
Mutagenesisi347 – 3471R → A: No effect. 1 Publication
Mutagenesisi354 – 3541W → A: No effect. 1 Publication
Mutagenesisi358 – 3581R → A: No effect. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 363363Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidasePRO_0000248996Add
BLAST

Proteomic databases

MaxQBiQ02890.
PeptideAtlasiQ02890.

Interactioni

Subunit structurei

Interacts with RAD23 subunit of 26S proteasome.3 Publications

Protein-protein interaction databases

BioGridi36085. 19 interactions.
DIPiDIP-4008N.
IntActiQ02890. 2 interactions.
MINTiMINT-574235.

Structurei

Secondary structure

1
363
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi13 – 3018Combined sources
Beta strandi31 – 333Combined sources
Helixi36 – 4813Combined sources
Helixi50 – 6516Combined sources
Helixi69 – 7810Combined sources
Helixi81 – 9414Combined sources
Beta strandi97 – 1004Combined sources
Helixi103 – 11816Combined sources
Beta strandi130 – 1323Combined sources
Beta strandi138 – 1469Combined sources
Helixi151 – 1533Combined sources
Beta strandi154 – 16512Combined sources
Turni166 – 1683Combined sources
Beta strandi171 – 1777Combined sources
Helixi180 – 1867Combined sources
Helixi191 – 20313Combined sources
Turni204 – 2063Combined sources
Beta strandi209 – 2146Combined sources
Turni215 – 2173Combined sources
Beta strandi218 – 2258Combined sources
Turni226 – 2294Combined sources
Beta strandi230 – 2356Combined sources
Turni236 – 2394Combined sources
Beta strandi240 – 2423Combined sources
Helixi246 – 2505Combined sources
Beta strandi258 – 2625Combined sources
Beta strandi265 – 2684Combined sources
Helixi270 – 2734Combined sources
Beta strandi275 – 2784Combined sources
Helixi286 – 30116Combined sources
Helixi306 – 32419Combined sources
Beta strandi325 – 3273Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1X3WX-ray3.00A8-342[»]
1X3ZX-ray2.80A8-342[»]
3ESWX-ray3.40A8-341[»]
ProteinModelPortaliQ02890.
SMRiQ02890. Positions 8-327.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ02890.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

GeneTreeiENSGT00390000006540.
HOGENOMiHOG000183313.
InParanoidiQ02890.
KOiK01456.
OMAiGRCGEWC.
OrthoDBiEOG7HMS8Q.

Family and domain databases

InterProiIPR018325. Rad4/PNGase_transGLS-fold.
IPR002931. Transglutaminase-like.
[Graphical view]
PfamiPF03835. Rad4. 1 hit.
[Graphical view]
SMARTiSM00460. TGc. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q02890-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGEVYEKNNI DFDSIAKMLL IKYKDFILSK FKKAAPVENI RFQNLVHTNQ
60 70 80 90 100
FAQGVLGQSQ HLCTVYDNPS WHSIVLETLD LDLIYKNVDK EFAKDGHAEG
110 120 130 140 150
ENIYTDYLVK ELLRYFKQDF FKWCNKPDCN HCGQNTSENM TPLGSQGPNG
160 170 180 190 200
EESKFNCGTV EIYKCNRCGN ITRFPRYNDP IKLLETRKGR CGEWCNLFTL
210 220 230 240 250
ILKSFGLDVR YVWNREDHVW CEYFSNFLNR WVHVDSCEQS FDQPYIYSIN
260 270 280 290 300
WNKKMSYCIA FGKDGVVDVS KRYILQNELP RDQIKEEDLK FLCQFITKRL
310 320 330 340 350
RYSLNDDEIY QLACRDEQEQ IELIRGKTQE TKSESVSAAS KSSNRGRESG
360
SADWKAQRGE DGK
Length:363
Mass (Da):42,485
Last modified:November 1, 1996 - v1
Checksum:i004F3E3E07C3B954
GO

Mass spectrometryi

Molecular mass is 43208 Da from positions 1 - 363. Determined by MALDI. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U43281 Genomic DNA. Translation: AAB68203.1.
BK006949 Genomic DNA. Translation: DAA11337.1.
PIRiS61970.
RefSeqiNP_015229.1. NM_001183910.1.

Genome annotation databases

EnsemblFungiiYPL096W; YPL096W; YPL096W.
GeneIDi856009.
KEGGisce:YPL096W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U43281 Genomic DNA. Translation: AAB68203.1.
BK006949 Genomic DNA. Translation: DAA11337.1.
PIRiS61970.
RefSeqiNP_015229.1. NM_001183910.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1X3WX-ray3.00A8-342[»]
1X3ZX-ray2.80A8-342[»]
3ESWX-ray3.40A8-341[»]
ProteinModelPortaliQ02890.
SMRiQ02890. Positions 8-327.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi36085. 19 interactions.
DIPiDIP-4008N.
IntActiQ02890. 2 interactions.
MINTiMINT-574235.

Proteomic databases

MaxQBiQ02890.
PeptideAtlasiQ02890.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYPL096W; YPL096W; YPL096W.
GeneIDi856009.
KEGGisce:YPL096W.

Organism-specific databases

EuPathDBiFungiDB:YPL096W.
SGDiS000006017. PNG1.

Phylogenomic databases

GeneTreeiENSGT00390000006540.
HOGENOMiHOG000183313.
InParanoidiQ02890.
KOiK01456.
OMAiGRCGEWC.
OrthoDBiEOG7HMS8Q.

Enzyme and pathway databases

BioCyciYEAST:YPL096W-MONOMER.
BRENDAi3.5.1.52. 984.

Miscellaneous databases

EvolutionaryTraceiQ02890.
NextBioi980893.
PROiQ02890.

Family and domain databases

InterProiIPR018325. Rad4/PNGase_transGLS-fold.
IPR002931. Transglutaminase-like.
[Graphical view]
PfamiPF03835. Rad4. 1 hit.
[Graphical view]
SMARTiSM00460. TGc. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI."
    Bussey H., Storms R.K., Ahmed A., Albermann K., Allen E., Ansorge W., Araujo R., Aparicio A., Barrell B.G., Badcock K., Benes V., Botstein D., Bowman S., Brueckner M., Carpenter J., Cherry J.M., Chung E., Churcher C.M.
    , Coster F., Davis K., Davis R.W., Dietrich F.S., Delius H., DiPaolo T., Dubois E., Duesterhoeft A., Duncan M., Floeth M., Fortin N., Friesen J.D., Fritz C., Goffeau A., Hall J., Hebling U., Heumann K., Hilbert H., Hillier L.W., Hunicke-Smith S., Hyman R.W., Johnston M., Kalman S., Kleine K., Komp C., Kurdi O., Lashkari D., Lew H., Lin A., Lin D., Louis E.J., Marathe R., Messenguy F., Mewes H.-W., Mirtipati S., Moestl D., Mueller-Auer S., Namath A., Nentwich U., Oefner P., Pearson D., Petel F.X., Pohl T.M., Purnelle B., Rajandream M.A., Rechmann S., Rieger M., Riles L., Roberts D., Schaefer M., Scharfe M., Scherens B., Schramm S., Schroeder M., Sdicu A.-M., Tettelin H., Urrestarazu L.A., Ushinsky S., Vierendeels F., Vissers S., Voss H., Walsh S.V., Wambutt R., Wang Y., Wedler E., Wedler H., Winnett E., Zhong W.-W., Zollner A., Vo D.H., Hani J.
    Nature 387:103-105(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  2. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  3. "PNG1, a yeast gene encoding a highly conserved peptide:N-glycanase."
    Suzuki T., Park H., Hollingsworth N.M., Sternglanz R., Lennarz W.J.
    J. Cell Biol. 149:1039-1052(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, MUTAGENESIS OF HIS-218.
  4. "Rad23 provides a link between the Png1 deglycosylating enzyme and the 26 S proteasome in yeast."
    Suzuki T., Park H., Kwofie M.A., Lennarz W.J.
    J. Biol. Chem. 276:21601-21607(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RAD23.
  5. "Site-directed mutagenesis study of yeast peptide:N-glycanase. Insight into the reaction mechanism of deglycosylation."
    Katiyar S., Suzuki T., Balgobin B.J., Lennarz W.J.
    J. Biol. Chem. 277:12953-12959(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF TRP-123; CYS-129; CYS-132; CYS-165; CYS-168; PHE-174; TYR-177; ARG-187; GLY-189; CYS-191; TRP-194; PHE-198; THR-199; LYS-203; GLY-206; ARG-210; VAL-212; HIS-218; TRP-220; GLU-222; PHE-224; ARG-230; VAL-234; ASP-235; ASP-242; TRP-251; LYS-253; TYR-257; PHE-261; ASP-264; VAL-266; ASP-268; TYR-273; ARG-281; ARG-347; TRP-354 AND ARG-358.
  6. "Free-oligosaccharide control in the yeast Saccharomyces cerevisiae: roles for peptide:N-glycanase (Png1p) and vacuolar mannosidase (Ams1p)."
    Chantret I., Frenoy J.-P., Moore S.E.H.
    Biochem. J. 373:901-908(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  7. "A role for N-glycanase in the cytosolic turnover of glycoproteins."
    Hirsch C., Blom D., Ploegh H.L.
    EMBO J. 22:1036-1046(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  8. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
  10. "The N-terminus of yeast peptide: N-glycanase interacts with the DNA repair protein Rad23."
    Biswas S., Katiyar S., Li G., Zhou X., Lennarz W.J., Schindelin H.
    Biochem. Biophys. Res. Commun. 323:149-155(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RAD23.
  11. "Yeast N-glycanase distinguishes between native and non-native glycoproteins."
    Hirsch C., Misaghi S., Blom D., Pacold M.E., Ploegh H.L.
    EMBO Rep. 5:201-206(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  12. "Using a small molecule inhibitor of peptide: N-glycanase to probe its role in glycoprotein turnover."
    Misaghi S., Pacold M.E., Blom D., Ploegh H.L., Korbel G.A.
    Chem. Biol. 11:1677-1687(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: MASS SPECTROMETRY, ENZYME REGULATION.
  13. "Misfolding of glycoproteins is a prerequisite for peptide: N-glycanase mediated deglycosylation."
    Joshi S., Katiyar S., Lennarz W.J.
    FEBS Lett. 579:823-826(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  14. "Site-specific labeling of cytoplasmic peptide: N-glycanase by N,N'-diacetylchitobiose-related compounds."
    Suzuki T., Hara I., Nakano M., Zhao G., Lennarz W.J., Schindelin H., Taniguchi N., Totani K., Matsuo I., Ito Y.
    J. Biol. Chem. 281:22152-22160(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION.
  15. "The Png1-Rad23 complex regulates glycoprotein turnover."
    Kim I., Ahn J., Liu C., Tanabe K., Apodaca J., Suzuki T., Rao H.
    J. Cell Biol. 172:211-219(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  16. "z-VAD-fmk inhibits peptide:N-glycanase and may result in ER stress."
    Misaghi S., Korbel G.A., Kessler B., Spooner E., Ploegh H.L.
    Cell Death Differ. 13:163-165(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: ENZYME REGULATION.
  17. "Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins."
    Lee J.-H., Choi J.M., Lee C., Yi K.J., Cho Y.
    Proc. Natl. Acad. Sci. U.S.A. 102:9144-9149(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 8-342 IN COMPLEX WITH RAD23 AND SUCROSE, COFACTOR, ZINC-BINDING.

Entry informationi

Entry nameiPNG1_YEAST
AccessioniPrimary (citable) accession number: Q02890
Secondary accession number(s): D6W3S1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 5, 2006
Last sequence update: November 1, 1996
Last modified: May 11, 2016
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 4850 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XVI
    Yeast (Saccharomyces cerevisiae) chromosome XVI: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.