Q9JI78 (NGLY1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Short name=PNGase
Short name=mPNGase
EC=3.5.1.52

Alternative name(s):
N-glycanase 1
Peptide:N-glycanase

Gene names

Name:

Ngly1

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	651 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.6 Ref.7 Ref.9
Catalytic activity	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.
Cofactor	Binds 1 zinc ion per subunit. Ref.14
Enzyme regulation	Inhibited by Z-VAD-fmk, a well-known caspase inhibitor, which inhibits enzyme activity through covalent binding of the carbohydrate to the single Cys-306 residue. Ref.8
Subunit structure	Component of a complex required to couple retrotranslocation, ubiquitination and deglycosylation composed of NGLY1, SAKS1, AMFR, VCP and RAD23B. Interacts with the proteasome components RAD23B and PSMC1. Interacts with directly with VCP. Interacts with DERL1, bringing it close to the endoplasmic reticulum membrane. Interacts with SAKS1. Ref.6 Ref.9 Ref.10 Ref.11 Ref.13
Subcellular location	Cytoplasm Ref.6 Ref.7 Ref.10.
Tissue specificity	Ubiquitously expressed with highest level in testis. Ref.2 Ref.6
Domain	The PUB domain mediates the interaction with VCP. Ref.13
Sequence similarities	Belongs to the transglutaminase-like superfamily. PNGase family. Contains 1 PAW domain. Contains 1 PUB (PUG) domain.
Biophysicochemical properties	Kinetic parameters: KM=114 µM for fetuin glycopeptide I Ref.5 Vmax=0.0964 nmol/min/mg enzyme with fetuin glycopeptide I as substrate

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Metal-binding Zinc
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	glycoprotein catabolic process Inferred from direct assay Ref.9. Source: UniProtKB
Cellular_component	cytoplasm Inferred from direct assay Ref.9. Source: UniProtKB nucleus Inferred from sequence or structural similarity Ref.1. Source: MGI
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity Inferred from sequence or structural similarity Ref.1. Source: MGI
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
Amfr	Q9R049	5	EBI-3648128,EBI-3648125
Vcp	Q01853	3	EBI-3648128,EBI-80597

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 651

651

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

PRO_0000248973

Regions

Domain

30 – 91

62

PUB

Domain

451 – 651

201

PAW

Sites

Active site

306

1

Nucleophile

Active site

333

1

Active site

350

1

Metal binding

247

1

Zinc

Metal binding

250

1

Zinc

Metal binding

280

1

Zinc

Metal binding

283

1

Zinc

Experimental info

Mutagenesis

41

1

N → P: Abolishes interaction with VCP. Ref.13

Mutagenesis

58

1

N → A: Does not affect the interaction with VCP. Ref.13

Mutagenesis

79 – 80

2

GF → AA: Abolishes interaction with VCP.

Mutagenesis

306

1

C → A: Abolishes enzyme activity. Ref.7

Sequence conflict

509

1

I → T in AAF74723. Ref.1

Sequence conflict

509

1

I → T in AAP03060. Ref.2

Secondary structure

1

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651

Helix Strand Turn

Details...

Helix

15 – 20

6

Helix

25 – 43

19

Beta strand

45 – 47

3

Helix

49 – 52

4

Beta strand

53 – 55

3

Helix

59 – 64

6

Turn

65 – 67

3

Helix

71 – 78

8

Beta strand

84 – 88

5

Helix

95 – 109

15

Helix

167 – 180

14

Helix

181 – 183

3

Helix

185 – 194

10

Helix

197 – 211

15

Helix

223 – 236

14

Turn

248 – 250

3

Beta strand

255 – 261

7

Helix

266 – 269

4

Beta strand

275 – 280

6

Turn

281 – 284

4

Beta strand

285 – 290

6

Helix

295 – 301

7

Beta strand

303 – 305

3

Helix

306 – 319

14

Beta strand

324 – 329

6

Turn

330 – 332

3

Beta strand

333 – 340

8

Turn

341 – 344

4

Beta strand

345 – 350

6

Turn

351 – 354

4

Beta strand

355 – 357

3

Helix

359 – 361

3

Turn

362 – 365

4

Beta strand

373 – 376

4

Beta strand

381 – 383

3

Helix

385 – 388

4

Helix

392 – 398

7

Helix

404 – 419

16

Helix

424 – 441

18

Beta strand

458 – 462

5

Helix

482 – 487

6

Beta strand

489 – 495

7

Turn

496 – 499

4

Beta strand

500 – 503

4

Helix

504 – 506

3

Beta strand

509 – 513

5

Helix

514 – 517

4

Beta strand

519 – 529

11

Turn

530 – 533

4

Beta strand

534 – 539

6

Beta strand

544 – 553

10

Helix

555 – 557

3

Beta strand

559 – 567

9

Beta strand

569 – 572

4

Beta strand

577 – 583

7

Beta strand

588 – 591

4

Beta strand

598 – 600

3

Turn

602 – 605

4

Beta strand

607 – 616

10

Helix

620 – 625

6

Beta strand

626 – 633

8

Beta strand

641 – 650

10

Sequences

	Sequence		Length	Mass (Da)
	Q9JI78 [UniParc]. Last modified September 5, 2006. Version 2. Checksum: F9D7A35726482F81	FASTA	651	74,275
	10 20 30 40 50 60 MASATLGSSS SSASPAVAEL CQNTPETFLE ASKLLLTYAD NILRNPSDEK YRSIRIGNTA 70 80 90 100 110 120 FSTRLLPVRG AVECLFEMGF EEGETHLIFP KKASVEQLQK IRDLIAIERS SRLDGSSKKV 130 140 150 160 170 180 QFSQHPAAAK LPLEQSEDPA GLIRHSGNQT GQLPSLPSAP MVVGDSTILK VLQSNIQHVQ 190 200 210 220 230 240 LYENPVLQEK ALTCIPVSEL KRKAQEKLFR ARKLDKGTNV SDEDFLLLEL LHWFKEEFFR 250 260 270 280 290 300 WVNNIVCSKC GGETRSRDEA LLPNDDELKW GAKNVENHYC DACQLSNRFP RYNNPEKLLE 310 320 330 340 350 360 TRCGRCGEWA NCFTLCCRAL GFEARYVWDY TDHVWTEVYS PSQQRWLHCD ACEDVCDKPL 370 380 390 400 410 420 LYEIGWGKKL SYIIAFSKDE VVDVTWRYSC KHDEVMSRRT KVKEELLRET INGLNKQRQL 430 440 450 460 470 480 SLSESRRKEL LQRIIVELVE FISPKTPRPG ELGGRVSGSL AWRVARGETG LERKEILFIP 490 500 510 520 530 540 SENEKISKQF HLRYDIVRDR YIRVSDNNIN ISGWENGVWK MESIFRKVEK DWNMVYLARK 550 560 570 580 590 600 EGSSFAYISW KFECGSAGLK VDTVSIRTSS QSFESGSVRW KLRSETAQVN LLGDKNLRSY 610 620 630 640 650 NDFSGATEVT LEAELSRGDG DVAWQHTQLF RQSLNDSGEN GLEIIITFND L

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"Ngly1, a mouse gene encoding a deglycosylating enzyme implicated in proteasomal degradation: expression, genomic organization, and chromosomal mapping." Suzuki T., Kwofie M.A., Lennarz W.J. Biochem. Biophys. Res. Commun. 304:326-332(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], TISSUE SPECIFICITY. Strain: 129/SvJ.
[3]	"The transcriptional landscape of the mammalian genome." Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: C57BL/6J. Tissue: Head.
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Eye.
[5]	"Purification and enzymatic properties of peptide:N-glycanase from C3H mouse-derived L-929 fibroblast cells. Possible widespread occurrence of post-translational remodification of proteins by N-deglycosylation." Suzuki T., Seko A., Kitajima K., Inoue Y., Inoue S. J. Biol. Chem. 269:17611-17618(1994) [PubMed] [Europe PMC] [Abstract] Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
[6]	"Identification of proteins that interact with mammalian peptide:N-glycanase and implicate this hydrolase in the proteasome-dependent pathway for protein degradation." Park H., Suzuki T., Lennarz W.J. Proc. Natl. Acad. Sci. U.S.A. 98:11163-11168(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH RAD23B; PSMC1 AND SAKS1.
[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, SUBCELLULAR LOCATION, MUTAGENESIS OF CYS-306.
[8]	"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: ENZYME REGULATION.
[9]	"A complex between peptide:N-glycanase and two proteasome-linked proteins suggests a mechanism for the degradation of misfolded glycoproteins." Katiyar S., Li G., Lennarz W.J. Proc. Natl. Acad. Sci. U.S.A. 101:13774-13779(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH RAD23B AND PSMC1.
[10]	"The retrotranslocation protein derlin-1 binds peptide:N-glycanase to the endoplasmic reticulum." Katiyar S., Joshi S., Lennarz W.J. Mol. Biol. Cell 16:4584-4594(2005) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, INTERACTION WITH DERL1.
[11]	"Multiple modes of interaction of the deglycosylation enzyme, mouse peptide N-glycanase, with the proteasome." Li G., Zhou X., Zhao G., Schindelin H., Lennarz W.J. Proc. Natl. Acad. Sci. U.S.A. 102:15809-15814(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PSMC1; RAD23B AND VCP.
[12]	Erratum Li G., Zhou X., Zhao G., Schindelin H., Lennarz W.J. Proc. Natl. Acad. Sci. U.S.A. 103:1153-1153(2006)
[13]	"The AAA ATPase p97 links peptide N-glycanase to the endoplasmic reticulum-associated E3 ligase autocrine motility factor receptor." Li G., Zhao G., Zhou X., Schindelin H., Lennarz W.J. Proc. Natl. Acad. Sci. U.S.A. 103:8348-8353(2006) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH AMFR; PSMC1; SAKS1; RAD23B AND VCP, DOMAIN, MUTAGENESIS OF ASN-41; ASN-58 AND 79-GLY-PHE-80.
[14]	"Structure of the mouse peptide N-glycanase-HR23 complex suggests co-evolution of the endoplasmic reticulum-associated degradation and DNA repair pathways." Zhao G., Zhou X., Wang L., Li G., Kisker C., Lennarz W.J., Schindelin H. J. Biol. Chem. 281:13751-13761(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 164-450 IN COMPLEX WITH RAD23 AND Z-VAD-FMK, COFACTOR, ZINC-BINDING.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF250927 mRNA. Translation: AAF74723.1.
AY225417 Genomic DNA. Translation: AAP03060.1.
AK003279 mRNA. Translation: BAB22686.1.
AK028248 mRNA. Translation: BAC25839.1.
BC028961 mRNA. Translation: AAH28961.1.

IPI

IPI00331613.

RefSeq

NP_067479.2. NM_021504.3.

UniGene

Mm.258381.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2D5U	NMR	-	A	1-119	[»]
2F4M	X-ray	1.85	A	164-450	[»]
2F4O	X-ray	2.26	A	164-450	[»]
2G9F	X-ray	1.90	A	451-651	[»]
2G9G	X-ray	2.00	A	451-651	[»]
2HPJ	X-ray	1.70	A	12-110	[»]
2HPL	X-ray	1.80	A	12-111	[»]
2I74	X-ray	1.75	A/B	471-651	[»]

ProteinModelPortal

Q9JI78.

SMR

Q9JI78. Positions 12-110, 164-450, 472-651.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9JI78. 3 interactions.

PTM databases

PhosphoSite

Q9JI78.

Proteomic databases

PaxDb

Q9JI78.

PRIDE

Q9JI78.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000022310; ENSMUSP00000022310; ENSMUSG00000021785.

GeneID

59007.

KEGG

mmu:59007.

UCSC

uc007sgz.1. mouse.

Organism-specific databases

CTD

55768.

MGI

MGI:1913276. Ngly1.

Phylogenomic databases

eggNOG

NOG307426.

GeneTree

ENSGT00390000006540.

HOGENOM

HOG000247069.

HOVERGEN

HBG082026.

InParanoid

Q9JI78.

KO

K01456.

OMA

CQNTPET.

OrthoDB

EOG4SF95F.

Gene expression databases

Bgee

Q9JI78.

CleanEx

MM_NGLY1.

Genevestigator

Q9JI78.

GermOnline

ENSMUSG00000021785. Mus musculus.

Family and domain databases

InterPro

IPR008979. Galactose-bd-like.
IPR006588. Peptide_N_glycanase_PAW_dom.
IPR018997. PUB_domain.
IPR006567. PUG-dom.
IPR002931. Transglutaminase-like.
[Graphical view]

Pfam

PF04721. DUF750. 1 hit.
PF09409. PUB. 1 hit.
PF01841. Transglut_core. 1 hit.
[Graphical view]

SMART

SM00613. PAW. 1 hit.
SM00580. PUG. 1 hit.
SM00460. TGc. 1 hit.
[Graphical view]

SUPFAM

SSF49785. Gal_bind_like. 1 hit.

PROSITE

PS51398. PAW. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9JI78.

NextBio

314538.

SOURCE

Search...

Entry information

Entry name

NGLY1_MOUSE

Accession

Primary (citable) accession number: Q9JI78
Secondary accession number(s): Q8K113, Q9CTK3

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 5, 2006
Last sequence update:	September 5, 2006
Last modified:	May 1, 2013
This is version 79 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program