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P21163

- PNGF_ELIMR

UniProt

P21163 - PNGF_ELIMR

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Protein

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

Gene
ngl, png
Organism
Elizabethkingia miricola (Chryseobacterium miricola)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Cleaves an entire glycan from a glycoprotein. Requires that the glycosylated asparagine moiety (reaction 1) be substituted on its amino (R1) and carboxyl (R2) terminus with a polypeptide chain.

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.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei100 – 1001
Active sitei158 – 1581
Active sitei246 – 2461

GO - Molecular functioni

  1. oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen Source: InterPro
  2. peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity Source: UniProtKB-EC
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Names & Taxonomyi

Protein namesi
Recommended name:
Peptide-N(4)-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F (EC:3.5.1.52)
Short name:
PNGase F
Alternative name(s):
Glycopeptide N-glycosidase
N-glycanase
Gene namesi
Name:ngl
Synonyms:png
OrganismiElizabethkingia miricola (Chryseobacterium miricola)
Taxonomic identifieri172045 [NCBI]
Taxonomic lineageiBacteriaBacteroidetesFlavobacteriiaFlavobacterialesFlavobacteriaceaeElizabethkingia

Pathology & Biotechi

Biotechnological usei

Widely used for the removal of N-glycans from glycoproteinss and glycopeptides in laboratory.

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi100 – 1001D → N: Complete loss of activity.
Mutagenesisi158 – 1581E → Q: Loss of activity.
Mutagenesisi246 – 2461E → Q: Loss of activity.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 40401 PublicationAdd
BLAST
Chaini41 – 354314Peptide-N(4)-(N-acetyl-beta-D-glucosaminyl)asparagine amidase FPRO_0000022079Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi91 ↔ 961 Publication
Disulfide bondi244 ↔ 2481 Publication
Disulfide bondi271 ↔ 2921 Publication

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Monomer.

Structurei

Secondary structure

1
354
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi46 – 505
Beta strandi54 – 574
Beta strandi60 – 623
Beta strandi65 – 739
Beta strandi80 – 8910
Helixi92 – 943
Beta strandi102 – 1087
Turni110 – 1123
Beta strandi115 – 1228
Beta strandi125 – 1273
Beta strandi132 – 1343
Beta strandi136 – 1394
Helixi141 – 1433
Turni144 – 1463
Beta strandi147 – 15711
Beta strandi165 – 17612
Beta strandi181 – 19111
Helixi195 – 1973
Beta strandi198 – 2036
Beta strandi210 – 2145
Beta strandi220 – 23112
Beta strandi233 – 2386
Turni239 – 2413
Beta strandi242 – 2454
Beta strandi250 – 2567
Beta strandi259 – 2668
Helixi271 – 2733
Beta strandi300 – 3034
Helixi306 – 3083
Beta strandi311 – 3188
Beta strandi326 – 3283
Beta strandi332 – 34514
Beta strandi351 – 3533

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1PGSX-ray1.80A41-354[»]
1PNFX-ray2.00A41-354[»]
1PNGX-ray2.20A41-354[»]
ProteinModelPortaliP21163.
SMRiP21163. Positions 41-354.

Miscellaneous databases

EvolutionaryTraceiP21163.

Family & Domainsi

Keywords - Domaini

Signal

Family and domain databases

Gene3Di2.60.120.230. 2 hits.
InterProiIPR014784. Cu2_ascorb_mOase-like_C.
IPR008977. PHM/PNGase_F_dom.
IPR015197. PngaseF_C.
IPR015196. PngaseF_N.
[Graphical view]
PfamiPF09113. N-glycanase_C. 1 hit.
PF09112. N-glycanase_N. 1 hit.
[Graphical view]
SUPFAMiSSF49742. SSF49742. 2 hits.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P21163-1 [UniParc]FASTAAdd to Basket

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MRKLLIFSIS AYLMAGIVSC KGVDSATPVT EDRLALNAVN APADNTVNIK    50
TFDKVKNAFG DGLSQSAEGT FTFPADVTTV KTIKMFIKNE CPNKTCDEWD 100
RYANVYVKNK TTGEWYEIGR FITPYWVGTE KLPRGLEIDV TDFKSLLSGN 150
TELKIYTETW LAKGREYSVD FDIVYGTPDY KYSAVVPVIQ YNKSSIDGVP 200
YGKAHTLGLK KNIQLPTNTE KAYLRTTISG WGHAKPYDAG SRGCAEWCFR 250
THTIAINNAN TFQHQLGALG CSANPINNQS PGNWAPDRAG WCPGMAVPTR 300
IDVLNNSLTG STFSYEYKFQ SWTNNGTNGD AFYAISSFVI AKSNTPISAP 350
VVTN 354
Length:354
Mass (Da):39,032
Last modified:November 1, 1991 - v2
Checksum:i22CF510F77C22539
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti33 – 331R → G in AAA85323. 1 Publication
Sequence conflicti160 – 1601W → C in AAA24932. 1 Publication
Sequence conflicti283 – 2831N → I in AAA85323. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J05449 mRNA. Translation: AAA85323.1.
J05411 Genomic DNA. Translation: AAA24932.1.
M57237 Genomic DNA. Translation: AAA24928.1. Sequence problems.
PIRiA38365. PNFMGF.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J05449 mRNA. Translation: AAA85323.1 .
J05411 Genomic DNA. Translation: AAA24932.1 .
M57237 Genomic DNA. Translation: AAA24928.1 . Sequence problems.
PIRi A38365. PNFMGF.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1PGS X-ray 1.80 A 41-354 [» ]
1PNF X-ray 2.00 A 41-354 [» ]
1PNG X-ray 2.20 A 41-354 [» ]
ProteinModelPortali P21163.
SMRi P21163. Positions 41-354.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P21163.

Family and domain databases

Gene3Di 2.60.120.230. 2 hits.
InterProi IPR014784. Cu2_ascorb_mOase-like_C.
IPR008977. PHM/PNGase_F_dom.
IPR015197. PngaseF_C.
IPR015196. PngaseF_N.
[Graphical view ]
Pfami PF09113. N-glycanase_C. 1 hit.
PF09112. N-glycanase_N. 1 hit.
[Graphical view ]
SUPFAMi SSF49742. SSF49742. 2 hits.
ProtoNeti Search...

Publicationsi

  1. "Molecular cloning and amino acid sequence of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase from flavobacterium meningosepticum."
    Tarentino A.L., Quinones G., Trumble A., Changchien L.-M., Duceman B., Maley F., Plummer T.H. Jr.
    J. Biol. Chem. 265:6961-6966(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
  2. "Cloning and expression of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F in Escherichia coli."
    Barsomian G.D., Johnson T.L., Borowski M., Denman J., Ollington J.F., Hirani S., McNeilly D.S., Rasmussen J.R.
    J. Biol. Chem. 265:6967-6972(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 41-61.
    Strain: ATCC 33958.
  3. "Molecular cloning and heterologous expression of N-glycosidase F from Flavobacterium meningosepticum."
    Lemp D., Haselbeck A., Klebl F.
    J. Biol. Chem. 265:15606-15610(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  4. "Crystal structure of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F at 2.2-A resolution."
    Kuhn P., Tarantino A.L., Plummer T.H. Jr., van Roey P.
    Biochemistry 33:11699-11706(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
  5. "The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum."
    Norris G.E., Stillman T.J., Anderson B.F., Baker E.N.
    Structure 2:1049-1059(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
  6. "Active site and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F."
    Kuhn P., Guan C., Cui T., Tarentino A.L., Plummer T.H. Jr., van Roey P.
    J. Biol. Chem. 270:29493-29497(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), MUTAGENESIS.

Entry informationi

Entry nameiPNGF_ELIMR
AccessioniPrimary (citable) accession number: P21163
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: November 1, 1991
Last modified: October 16, 2013
This is version 89 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

PNGase F binds primarily to the polypeptide chain around the glycosamine junction including the inner di-N-acetylchitobiose core on the carbohydrate moiety.

Caution

Submitted as Flavobacterium meningosepticum ATCC 33958 by the authors and identified as Elizabethkingia miricola by ATCC Catalog.

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references

External Data

Dasty 3

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