P21163 (PNGF_ELIMR) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Alternative name(s):
Glycopeptide N-glycosidase
N-glycanase

Gene names

Name:	ngl
Synonyms:	png

Organism

Elizabethkingia miricola (Chryseobacterium miricola)

Taxonomic identifier

172045 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Bacteroidetes/Chlorobi group › Bacteroidetes › Flavobacteriia › Flavobacteriales › Flavobacteriaceae › Elizabethkingia

Protein attributes

Sequence length	354 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 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.
Subunit structure	Monomer.
Biotechnological use	Widely used for the removal of N-glycans from glycoproteinss and glycopeptides in laboratory.
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.

Ontologies

Keywords
Domain	Signal
Molecular function	Hydrolase
PTM	Disulfide bond
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Molecular_function	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 Inferred from electronic annotation. Source: InterPro peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 40

40

Ref.2

Chain

41 – 354

314

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

PRO_0000022079

Sites

Active site

100

1

Active site

158

1

Active site

246

1

Amino acid modifications

Disulfide bond

91 ↔ 96

Ref.4

Disulfide bond

244 ↔ 248

Ref.4

Disulfide bond

271 ↔ 292

Ref.4

Experimental info

Mutagenesis

100

1

D → N: Complete loss of activity.

Mutagenesis

158

1

E → Q: Loss of activity.

Mutagenesis

246

1

E → Q: Loss of activity.

Sequence conflict

33

1

R → G in AAA85323. Ref.1

Sequence conflict

160

1

W → C in AAA24932. Ref.2

Sequence conflict

283

1

N → I in AAA85323. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

354

Helix Strand Turn

Details...

Beta strand

46 – 50

5

Beta strand

54 – 57

4

Beta strand

60 – 62

3

Beta strand

65 – 73

9

Beta strand

80 – 89

10

Helix

92 – 94

3

Beta strand

102 – 108

7

Turn

110 – 112

3

Beta strand

115 – 122

8

Beta strand

125 – 127

3

Beta strand

132 – 134

3

Beta strand

136 – 139

4

Helix

141 – 143

3

Turn

144 – 146

3

Beta strand

147 – 157

11

Beta strand

165 – 176

12

Beta strand

181 – 191

11

Helix

195 – 197

3

Beta strand

198 – 203

6

Beta strand

210 – 214

5

Beta strand

220 – 231

12

Beta strand

233 – 238

6

Turn

239 – 241

3

Beta strand

242 – 245

4

Beta strand

250 – 256

7

Beta strand

259 – 266

8

Helix

271 – 273

3

Beta strand

300 – 303

4

Helix

306 – 308

3

Beta strand

311 – 318

8

Beta strand

326 – 328

3

Beta strand

332 – 345

14

Beta strand

351 – 353

3

Sequences

	Sequence		Length	Mass (Da)
	P21163 [UniParc]. Last modified November 1, 1991. Version 2. Checksum: 22CF510F77C22539	FASTA	354	39,032
	10 20 30 40 50 60 MRKLLIFSIS AYLMAGIVSC KGVDSATPVT EDRLALNAVN APADNTVNIK TFDKVKNAFG 70 80 90 100 110 120 DGLSQSAEGT FTFPADVTTV KTIKMFIKNE CPNKTCDEWD RYANVYVKNK TTGEWYEIGR 130 140 150 160 170 180 FITPYWVGTE KLPRGLEIDV TDFKSLLSGN TELKIYTETW LAKGREYSVD FDIVYGTPDY 190 200 210 220 230 240 KYSAVVPVIQ YNKSSIDGVP YGKAHTLGLK KNIQLPTNTE KAYLRTTISG WGHAKPYDAG 250 260 270 280 290 300 SRGCAEWCFR THTIAINNAN TFQHQLGALG CSANPINNQS PGNWAPDRAG WCPGMAVPTR 310 320 330 340 350 IDVLNNSLTG STFSYEYKFQ SWTNNGTNGD AFYAISSFVI AKSNTPISAP VVTN

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J05449 mRNA. Translation: AAA85323.1.
J05411 Genomic DNA. Translation: AAA24932.1.
M57237 Genomic DNA. Translation: AAA24928.1. Sequence problems.

PIR

PNFMGF. A38365.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P21163.

SMR

P21163. Positions 41-354.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

Gene3D

2.60.120.230. 2 hits.

InterPro

IPR014784. Cu2_ascorb_mOase-like_C.
IPR008977. PHM/PNGase_F_dom.
IPR015197. PngaseF_C.
IPR015196. PngaseF_N.
[Graphical view]

Pfam

PF09113. N-glycanase_C. 1 hit.
PF09112. N-glycanase_N. 1 hit.
[Graphical view]

SUPFAM

SSF49742. PHM_PNGase_F. 2 hits.

ProtoNet

Search...

Other

EvolutionaryTrace

P21163.

Entry information

Entry name

PNGF_ELIMR

Accession

Primary (citable) accession number: P21163

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	November 1, 1991
Last modified:	April 3, 2013
This is version 88 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program