EzCatDB: S00213
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeS00213
RLCP classification1.32.60200.73 : Hydrolysis
CATH domainDomain 13.20.20.80 : TIM BarrelCatalytic domain
E.C.3.2.1.96
CSA2ebn

CATH domainRelated DB codes (homologues)
3.20.20.80 : TIM BarrelS00202,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

Enzyme Name
UniProtKBKEGG

P04067P36911P36913
Protein nameEndo-beta-N-acetylglucosaminidase HEndo-beta-N-acetylglucosaminidase F1Endo-beta-N-acetylglucosaminidase F3mannosyl-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
SynonymsEC 3.2.1.96
Mannosyl-glycoprotein endo-beta-N-acetyl-glucosaminidase H
DI-N-acetylchitobiosyl beta-N-acetylglucosaminidase H
Endoglycosidase H
Endo H
EC 3.2.1.96
Mannosyl-glycoprotein endo-beta-N-acetyl-glucosaminidase F1
Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase F1
Endoglycosidase F1
EC 3.2.1.96
Mannosyl-glycoprotein endo-beta-N-acetyl-glucosaminidase F3
Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase F3
Endoglycosidase F3
PfamPF00704 (Glyco_hydro_18)
[Graphical view]
PF00704 (Glyco_hydro_18)
[Graphical view]
PF00704 (Glyco_hydro_18)
[Graphical view]
CAZyGH18 (Glycoside Hydrolase Family)
GH18 (Glycoside Hydrolase Family)
GH18 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00511N-Glycan degradation
MAP01032Glycan structures - degradation

UniProtKB:Accession NumberP04067P36911P36913
Entry nameEBAG_STRPLEBA1_FLAMEEBA3_FLAME
ActivityEndohydrolysis 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.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.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.
Subunit
Monomer.Monomer.
Subcellular location
Secreted.Secreted.
Cofactor



Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idL00065C00001L00066L00019I00112
CompoundHigh-mannose glycopeptide containing-{Man(GlcNAc)2}-Asn N-glycanH2OOligosaccharide(terminal-(Man)n-GlcNAc)Glycopeptide containing N4-(beta-N-Acetyl-D-glucosaminyl)-L-asparagine residueIntramolecular cyclic intermediate at reducing end of terminal-(Man)n-GlcNAc
Typeamide group,peptide/protein,polysaccharideH2Oamide group,polysaccharideamide group,carbohydrate,peptide/protein
ChEBI
15377



PubChem
962
22247451
91857880


             
1c3fAUnbound UnboundUnbound 
1c8xAUnbound UnboundUnbound 
1c8yAUnbound UnboundUnbound 
1c90AUnbound UnboundUnbound 
1c90BUnbound UnboundUnbound 
1c91AUnbound UnboundUnbound 
1c92AUnbound UnboundUnbound 
1c93AUnbound UnboundUnbound 
1edtAUnbound UnboundUnbound 
2ebnAUnbound UnboundUnbound 
1eokAUnbound UnboundUnbound 
1eomAUnbound Bound:NAG-MAN-MAN-NAG-GAL-MAN-NAG-GAL(chain B)Unbound 

Active-site residues
resource
literature [6], [9], [11], [12], [13]
pdbCatalytic residuescomment
          
1c3fA       ;GLU 132;TYR 196
mutant D130N
1c8xA       ;GLU 132;TYR 196
mutant D130E
1c8yA       ;GLU 132;TYR 196
mutant D130A
1c90AASP 130;       ;TYR 196
mutant E132Q
1c90BASP 130;       ;TYR 196
mutant E132Q
1c91AASP 130;       ;TYR 196
mutant E132D
1c92AASP 130;       ;TYR 196
mutant E132A
1c93A       ;       ;TYR 196
mutant D130N, E132Q
1edtAASP 130;GLU 132;TYR 196
 
2ebnAASP 130;GLU 132;TYR 199
 
1eokAASP 126;GLU 128;TYR 213
 
1eomAASP 126;GLU 128;TYR 213
 

References for Catalytic Mechanism
ReferencesSectionsNo. 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]
PubMed ID6437277
JournalAnal Biochem
Year1984
Volume141
Pages515-22
AuthorsTrimble RB, Maley F
TitleOptimizing hydrolysis of N-linked high-mannose oligosaccharides by endo-beta-N-acetylglucosaminidase H.
[2]
PubMed ID3093228
JournalEur J Biochem
Year1986
Volume159
Pages381-5
AuthorsBaussant T, Strecker G, Wieruszeski JM, Montreuil J, Michalski JC
TitleCatabolism of glycoprotein glycans. Characterization of a lysosomal endo-N-acetyl-beta-D-glucosaminidase specific for glycans with a terminal chitobiose residue.
[3]
PubMed ID3091595
JournalJ Biol Chem
Year1986
Volume261
Pages12000-5
AuthorsTrimble RB, Atkinson PH, Tarentino AL, Plummer TH Jr, Maley F, Tomer KB
TitleTransfer of glycerol by Endo-beta-N-acetylglucosaminidase F to oligosaccharides during chitobiose core cleavage.
[4]
PubMed ID1899092
JournalJ Biol Chem
Year1991
Volume266
Pages1646-51
AuthorsTrimble RB, Tarentino AL
TitleIdentification 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.
[5]
PubMed ID1740434
JournalJ Biol Chem
Year1992
Volume267
Pages3868-72
AuthorsTarentino AL, Quinones G, Schrader WP, Changchien LM, Plummer TH Jr
TitleMultiple endoglycosidase (Endo) F activities expressed by Flavobacterium meningosepticum. Endo F1: molecular cloning, primary sequence, and structural relationship to Endo H.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID95034840
PubMed ID7947807
JournalBiochemistry
Year1994
Volume33
Pages13989-96
AuthorsVan Roey P, Rao V, Plummer TH Jr, Tarentino AL
TitleCrystal structure of endo-beta-N-acetylglucosaminidase F1, an alpha/beta-barrel enzyme adapted for a complex substrate.
Related PDB2ebn
Related UniProtKBP36911
[7]
PubMed ID8133514
JournalJ Mol Biol
Year1994
Volume237
Pages157-9
AuthorsVan Roey P, Silva GH, Rao V, Plummer TH Jr, Tarentino AL, Guan C
TitleCrystallization and preliminary crystallographic analysis of two endo-beta-N-acetylglucosaminidases, endo H and endo F1.
[8]
CommentsX-ray crystallography (1.85 Angstroms)
Medline ID96096984
PubMed ID7495789
JournalBiochemistry
Year1995
Volume34
Pages15619-15623
AuthorsTerwisscha van Scheltinga AC, Armand S, Kalk KH, Isogai A, Henrissat B, Dijkstra BW
TitleStereochemistry of chitin hydrolysis by a plant chitinase/lysozyme and X-ray structure of a complex with allosamidin: evidence for substrate assisted catalysis.
[9]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID95393016
PubMed ID7663942
JournalStructure
Year1995
Volume3
Pages449-57
AuthorsRao V, Guan C, Van Roey P
TitleCrystal structure of endo-beta-N-acetylglucosaminidase H at 1.9 A resolution: active-site geometry and substrate recognition.
Related PDB1edt
Related UniProtKBP04067
[10]
PubMed ID8831791
JournalJ Mol Biol
Year1996
Volume262
Pages243-57
AuthorsTerwisscha van Scheltinga AC, Hennig M, Dijkstra BW
TitleThe 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.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 48-312 OF MUTANTS.
Medline ID20060985
PubMed ID10595536
JournalProtein Sci
Year1999
Volume8
Pages2338-46
AuthorsRao V, Cui T, Guan C, Van Roey P
TitleMutations of endo-beta-N-acetylglucosaminidase H active site residues Asp130 and Glu132: activities and conformations.
Related PDB1c3f,1c8x,1c8y,1c90,1c91,1c92,1c93
Related UniProtKBP04067
[12]
CommentsX-ray crystallography
PubMed ID10891067
JournalBiochemistry
Year2000
Volume39
Pages7878-85
AuthorsWaddling CA, Plummer TH Jr, Tarentino AL, Van Roey P
TitleStructural basis for the substrate specificity of endo-beta-N-acetylglucosaminidase F(3).
Related PDB1eok,1eom
[13]
CommentsX-ray crystallography
PubMed ID11560481
JournalBiochemistry
Year2001
Volume40
Pages11338-43
AuthorsPapanikolau Y, Prag G, Tavlas G, Vorgias CE, Oppenheim AB, Petratos K
TitleHigh resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis.
[14]
PubMed ID11514092
JournalBiochim Biophys Acta
Year2001
Volume1528
Pages9-14
AuthorsFujita M, Shoda S, Haneda K, Inazu T, Takegawa K, Yamamoto K
TitleA novel disaccharide substrate having 1,2-oxazoline moiety for detection of transglycosylating activity of endoglycosidases.
[15]
PubMed ID11515537
JournalBiosci Biotechnol Biochem
Year2001
Volume65
Pages1542-8
AuthorsFujita K, Nakatake R, Yamabe K, Watanabe A, Asada Y, Takegawa K
TitleIdentification of amino acid residues essential for the substrate specificity of Flavobacterium sp. endo-beta-N-acetylglucosaminidase.
[16]
CommentsClustering of structures
PubMed ID11742103
JournalProtein Eng
Year2001
Volume14
Pages845-55
AuthorsNagano N, Porter CT, Thornton JM
TitleThe (betaalpha)(8) glycosidases: sequence and structure analyses suggest distant evolutionary relationships.

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.

createdupdated
2004-07-162011-12-22


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.