DB code: S00213

RLCP classification 1.32.60200.73 : Hydrolysis
CATH domain 3.20.20.80 : TIM Barrel Catalytic domain
E.C. 3.2.1.96
CSA 2ebn
M-CSA 2ebn
MACiE

CATH domain Related DB codes (homologues)
3.20.20.80 : TIM Barrel S00202 S00210 S00748 S00906 S00907 S00911 S00912 S00915 M00134 M00160 D00479 S00204 S00205 S00206 S00207 S00203 S00208 S00209 S00211 S00214 M00113 T00307 D00165 D00166 D00169 D00176 D00501 D00502 D00503 D00844 D00861 D00864 M00026 M00112 M00193 M00346 T00057 T00062 T00063 T00066 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
P04067 Endo-beta-N-acetylglucosaminidase H
EC 3.2.1.96
Mannosyl-glycoprotein endo-beta-N-acetyl-glucosaminidase H
DI-N-acetylchitobiosyl beta-N-acetylglucosaminidase H
Endoglycosidase H
Endo H
GH18 (Glycoside Hydrolase Family 18)
PF00704 (Glyco_hydro_18)
[Graphical View]
P36911 Endo-beta-N-acetylglucosaminidase F1
EC 3.2.1.96
Mannosyl-glycoprotein endo-beta-N-acetyl-glucosaminidase F1
Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase F1
Endoglycosidase F1
GH18 (Glycoside Hydrolase Family 18)
PF00704 (Glyco_hydro_18)
[Graphical View]
P36913 Endo-beta-N-acetylglucosaminidase F3
EC 3.2.1.96
Mannosyl-glycoprotein endo-beta-N-acetyl-glucosaminidase F3
Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase F3
Endoglycosidase F3
GH18 (Glycoside Hydrolase Family 18)
PF00704 (Glyco_hydro_18)
[Graphical View]

KEGG enzyme name
mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
N,N'-diacetylchitobiosyl beta-N-acetylglucosaminidase
endo-beta-N-acetylglucosaminidase
mannosyl-glycoprotein endo-beta-N-acetylglucosamidase
di-N-acetylchitobiosyl beta-N-acetylglucosaminidase
endo-beta-acetylglucosaminidase
endo-beta-(1->4)-N-acetylglucosaminidase
mannosyl-glycoprotein 1,4-N-acetamidodeoxy-beta-D-glycohydrolase
endoglycosidase S
endo-N-acetyl-beta-D-glucosaminidase
endo-N-acetyl-beta-glucosaminidase
endo-beta-N-acetylglucosaminidase D
endo-beta-N-acetylglucosaminidase F
endo-beta-N-acetylglucosaminidase H
endo-beta-N-acetylglucosaminidase L
glycopeptide-D-mannosyl-4-N-(N-acetyl-D-glucosaminyl)2-asparagine1,4-N-acetyl-beta-glucosaminohydrolase
endoglycosidase H

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P04067 EBAG_STRPL Endohydrolysis of the N,N''-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -(Man(GlcNAc)(2))Asn-structure. One N-acetyl-D-glucosamine residue remains attached to the protein, the rest of the oligosaccharide is released intact.
P36911 EBA1_FLAME Endohydrolysis of the N,N''-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -(Man(GlcNAc)(2))Asn-structure. One N-acetyl-D-glucosamine residue remains attached to the protein, the rest of the oligosaccharide is released intact. Monomer. Secreted.
P36913 EBA3_FLAME Endohydrolysis of the N,N''-diacetylchitobiosyl unit in high-mannose glycopeptides and glycoproteins containing the -(Man(GlcNAc)(2))Asn-structure. One N-acetyl-D-glucosamine residue remains attached to the protein, the rest of the oligosaccharide is released intact. Monomer. Secreted.

KEGG Pathways
Map code Pathways E.C.
MAP00511 N-Glycan degradation
MAP01032 Glycan structures - degradation

Compound table
Substrates Products Intermediates
KEGG-id L00065 C00001 L00066 L00019 I00112
E.C.
Compound High-mannose glycopeptide containing-{Man(GlcNAc)2}-Asn N-glycan H2O Oligosaccharide(terminal-(Man)n-GlcNAc) Glycopeptide containing N4-(beta-N-Acetyl-D-glucosaminyl)-L-asparagine residue Intramolecular cyclic intermediate at reducing end of terminal-(Man)n-GlcNAc
Type amide group,peptide/protein,polysaccharide H2O amide group,polysaccharide amide group,carbohydrate,peptide/protein
ChEBI 15377
PubChem 22247451
962
91857880
1c3fA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1c8xA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1c8yA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1c90A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1c90B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1c91A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1c92A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1c93A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1edtA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2ebnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1eokA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1eomA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NAG-MAN-MAN-NAG-GAL-MAN-NAG-GAL (chain B) Unbound

Reference for Active-site residues
resource references E.C.
literature [6], [9], [11], [12], [13]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1c3fA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;GLU 132;TYR 196 mutant D130N
1c8xA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;GLU 132;TYR 196 mutant D130E
1c8yA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;GLU 132;TYR 196 mutant D130A
1c90A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 130;;TYR 196 mutant E132Q
1c90B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 130;;TYR 196 mutant E132Q
1c91A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 130;;TYR 196 mutant E132D
1c92A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 130;;TYR 196 mutant E132A
1c93A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ; ;TYR 196 mutant D130N, E132Q
1edtA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 130;GLU 132;TYR 196
2ebnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 130;GLU 132;TYR 199
1eokA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 126;GLU 128;TYR 213
1eomA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 126;GLU 128;TYR 213

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[6]
p.13992-13994
[8]
Fig.2, Fig.3, p.15621-15623
[9]
p.453-454
[11]
p.2344-2345
[12]
p.7882
[13]
Scheme 1, p.11342
[14]
Fig.7, p.13

References
[1]
Resource
Comments
Medline ID
PubMed ID 6437277
Journal Anal Biochem
Year 1984
Volume 141
Pages 515-22
Authors Trimble RB, Maley F
Title Optimizing hydrolysis of N-linked high-mannose oligosaccharides by endo-beta-N-acetylglucosaminidase H.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 3093228
Journal Eur J Biochem
Year 1986
Volume 159
Pages 381-5
Authors Baussant T, Strecker G, Wieruszeski JM, Montreuil J, Michalski JC
Title Catabolism of glycoprotein glycans. Characterization of a lysosomal endo-N-acetyl-beta-D-glucosaminidase specific for glycans with a terminal chitobiose residue.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 3091595
Journal J Biol Chem
Year 1986
Volume 261
Pages 12000-5
Authors Trimble RB, Atkinson PH, Tarentino AL, Plummer TH Jr, Maley F, Tomer KB
Title Transfer of glycerol by Endo-beta-N-acetylglucosaminidase F to oligosaccharides during chitobiose core cleavage.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 1899092
Journal J Biol Chem
Year 1991
Volume 266
Pages 1646-51
Authors Trimble RB, Tarentino AL
Title Identification of distinct endoglycosidase (endo) activities in Flavobacterium meningosepticum: endo F1, endo F2, and endo F3. Endo F1 and endo H hydrolyze only high mannose and hybrid glycans.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 1740434
Journal J Biol Chem
Year 1992
Volume 267
Pages 3868-72
Authors Tarentino AL, Quinones G, Schrader WP, Changchien LM, Plummer TH Jr
Title Multiple endoglycosidase (Endo) F activities expressed by Flavobacterium meningosepticum. Endo F1: molecular cloning, primary sequence, and structural relationship to Endo H.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID 95034840
PubMed ID 7947807
Journal Biochemistry
Year 1994
Volume 33
Pages 13989-96
Authors Van Roey P, Rao V, Plummer TH Jr, Tarentino AL
Title Crystal structure of endo-beta-N-acetylglucosaminidase F1, an alpha/beta-barrel enzyme adapted for a complex substrate.
Related PDB 2ebn
Related UniProtKB P36911
[7]
Resource
Comments
Medline ID
PubMed ID 8133514
Journal J Mol Biol
Year 1994
Volume 237
Pages 157-9
Authors Van Roey P, Silva GH, Rao V, Plummer TH Jr, Tarentino AL, Guan C
Title Crystallization and preliminary crystallographic analysis of two endo-beta-N-acetylglucosaminidases, endo H and endo F1.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-ray crystallography (1.85 Angstroms)
Medline ID 96096984
PubMed ID 7495789
Journal Biochemistry
Year 1995
Volume 34
Pages 15619-15623
Authors Terwisscha van Scheltinga AC, Armand S, Kalk KH, Isogai A, Henrissat B, Dijkstra BW
Title Stereochemistry of chitin hydrolysis by a plant chitinase/lysozyme and X-ray structure of a complex with allosamidin: evidence for substrate assisted catalysis.
Related PDB
Related UniProtKB
[9]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID 95393016
PubMed ID 7663942
Journal Structure
Year 1995
Volume 3
Pages 449-57
Authors Rao V, Guan C, Van Roey P
Title Crystal structure of endo-beta-N-acetylglucosaminidase H at 1.9 A resolution: active-site geometry and substrate recognition.
Related PDB 1edt
Related UniProtKB P04067
[10]
Resource
Comments
Medline ID
PubMed ID 8831791
Journal J Mol Biol
Year 1996
Volume 262
Pages 243-57
Authors Terwisscha van Scheltinga AC, Hennig M, Dijkstra BW
Title The 1.8 A resolution structure of hevamine, a plant chitinase/lysozyme, and analysis of the conserved sequence and structure motifs of glycosyl hydrolase family 18.
Related PDB
Related UniProtKB
[11]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 48-312 OF MUTANTS.
Medline ID 20060985
PubMed ID 10595536
Journal Protein Sci
Year 1999
Volume 8
Pages 2338-46
Authors Rao V, Cui T, Guan C, Van Roey P
Title Mutations of endo-beta-N-acetylglucosaminidase H active site residues Asp130 and Glu132: activities and conformations.
Related PDB 1c3f 1c8x 1c8y 1c90 1c91 1c92 1c93
Related UniProtKB P04067
[12]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10891067
Journal Biochemistry
Year 2000
Volume 39
Pages 7878-85
Authors Waddling CA, Plummer TH Jr, Tarentino AL, Van Roey P
Title Structural basis for the substrate specificity of endo-beta-N-acetylglucosaminidase F(3).
Related PDB 1eok 1eom
Related UniProtKB
[13]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11560481
Journal Biochemistry
Year 2001
Volume 40
Pages 11338-43
Authors Papanikolau Y, Prag G, Tavlas G, Vorgias CE, Oppenheim AB, Petratos K
Title High resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11514092
Journal Biochim Biophys Acta
Year 2001
Volume 1528
Pages 9-14
Authors Fujita M, Shoda S, Haneda K, Inazu T, Takegawa K, Yamamoto K
Title A novel disaccharide substrate having 1,2-oxazoline moiety for detection of transglycosylating activity of endoglycosidases.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11515537
Journal Biosci Biotechnol Biochem
Year 2001
Volume 65
Pages 1542-8
Authors Fujita K, Nakatake R, Yamabe K, Watanabe A, Asada Y, Takegawa K
Title Identification of amino acid residues essential for the substrate specificity of Flavobacterium sp. endo-beta-N-acetylglucosaminidase.
Related PDB
Related UniProtKB
[16]
Resource
Comments Clustering of structures
Medline ID
PubMed ID 11742103
Journal Protein Eng
Year 2001
Volume 14
Pages 845-55
Authors Nagano N, Porter CT, Thornton JM
Title The (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the glycosidase family-18.
This enzyme is homologous to other glycosidase family-18 enzynmes;chitinase (T00063, M00134 in EzCatDB) or hevamine(S00204 in EzCatDB).
Considering the similarity of the catalytic site to that of hevamine (S00204 in EzCatDB), the reaction mechanism must be similar to that of the enzyme.

Created Updated
2004-07-16 2011-12-22