EzCatDB: S00207

DB codeS00207
RLCP classification1.30.36210.971
CATH domainDomain 13.20.20.80Catalytic domain
E.C.3.2.1.39
CSA1ghs

CATH domainRelated DB codes (homologues)
3.20.20.80S00202,S00210,S00748,S00906,S00907,S00911,S00912,S00915,M00134,M00160,D00479,S00204,S00205,S00206,S00203,S00208,S00209,S00211,S00213,S00214,M00113,T00307,D00165,D00166,D00169,D00176,D00501,D00502,D00503,D00844,D00861,D00864,M00026,M00112,M00193,M00346,T00057,T00062,T00063,T00066,T00067

Enzyme Name
Swiss-protKEGG

P15737
Protein nameGlucan endo-1,3-beta-glucosidase GIIglucan endo-1,3-beta-D-glucosidase
endo-1,3-beta-glucanase
laminarinase
laminaranase
oligo-1,3-glucosidase
endo-1,3-beta-glucanase
callase
beta-1,3-glucanase
kitalase
1,3-beta-D-glucan 3-glucanohydrolase
endo-(1,3)-beta-D-glucanase
(1->3)-beta-glucan 3-glucanohydrolase
endo-1,3-beta-D-glucanase
endo-1,3-beta-glucosidase
1,3-beta-D-glucan glucanohydrolase
SynonymsEC 3.2.1.39
EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase GII
1->3)-beta-glucan endohydrolase GII) ((1->3)-beta-glucanase isoenzyme GII
Beta-1,3-endoglucanase GII

KEGG pathways
MAP codePathways
MAP00500Starch and sucrose metabolism

Swiss-prot:Accession NumberP15737
Entry nameE13B_HORVU
ActivityHydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans.
Subunit
Subcellular location
Cofactor


SubstratesProducts
KEGG-idC00965C00001C00771C00965
Compound1,3-beta-D-GlucanH2OLaminarin1,3-beta-D-Glucan
TypepolysaccharideH2Opolysaccharidepolysaccharide
1ghsAUnbound
UnboundUnbound
1ghsBUnbound
UnboundUnbound

Active-site residues
pdbCatalytic residues
1ghsAGLU 94;TYR 168;GLU 231
1ghsBGLU 94;TYR 168;GLU 231

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]

[4]

[5]p.115, Scheme12
[6]Fig.34

references
[1]
Commentscrystallization, preliminary X-ray analysis (1.8 angstroms)
PubMed ID8254681
JournalJ Mol Biol
Year1993
Volume234
Pages888-9
AuthorsChen L, Garrett TJ, Varghese JN, Fincher GB, Hoj PB
TitleCrystallization and preliminary X-ray analysis of (1,3)- and (1,3;1,4)-beta-D-glucanases from germinating barley.
[2]
Commentscatalytic amino acid residues
PubMed ID8514770
JournalJ Biol Chem
Year1993
Volume268
Pages13318-26
AuthorsChen L, Fincher GB, Hoj PB
TitleEvolution of polysaccharide hydrolase substrate specificity. Catalytic amino acids are conserved in barley 1,3-1,4- and 1,3-beta-glucanases.
[3]
CommentsX-ray crystallography (2.3 angstroms).
Medline ID94195828
PubMed ID8146192
JournalProc Natl Acad Sci USA
Year1994
Volume91
Pages2785-9
AuthorsVarghese JN, Garrett TPJ, Colman PM, Chen L, Hoej PB, Fincher GB
TitleThree-dimensional structures of two plant beta-glucan endohydrolases with distinct substrate specificities.
Related PDB1ghs
Related Swiss-protP15737
[4]
PubMed ID7729513
JournalFEBS Lett
Year1995
Volume362
Pages281-5
AuthorsJenkins J, Lo Leggio L, Harris G, Pickersgill R
TitleBeta-glucosidase, beta-galactosidase, family A cellulases, family F xylanases and two barley glycanases form a superfamily of enzymes with 8-fold beta/alpha architecture and with two conserved glutamates near the carboxy-terminal ends of beta-strands four and seven.
[5]
PubMed ID7492591
JournalBiochim Biophys Acta
Year1995
Volume1253
Pages112-6
AuthorsChen L, Sadek M, Stone BA, Brownlee RT, Fincher GB, Hoj PB
TitleStereochemical course of glucan hydrolysis by barley (1-->3)- and (1-->3, 1-->4)-beta-glucanases.
[6]
Commentsstructure-function relationships (review)
PubMed ID11554481
JournalPlant Mol Biol
Year2001
Volume47
Pages73-91
AuthorsHrmova M, Fincher GB
TitleStructure-function relationships of beta-D-glucan endo- and exohydrolases from higher plants.
[7]
PubMed ID12023973
JournalJ Biol Chem
Year2002
Volume277
Pages30102-11
AuthorsHrmova M, Imai T, Rutten SJ, Fairweather JK, Pelosi L, Bulone V, Driguez H, Fincher GB
TitleMutated varley (1,3)-beta-D-glucan endohydrolases synthesize crystalline (1,3)-beta-D-glucans.

comments
This enzyme belongs to the family-17 of glycosidase enzymes, a member family of 4/7 superfamily, which has got the catalytic residues at the C-terminal ends of beta-4 and beta-7 on the (alpha/beta)8 barrel fold.
Glu231 has been reported to be the nucleophilic residue of this enzyme (see [2]). In contrast, whilst the paper [2] indicated experimentally that Glu288 might be a general acid that protonates the glycosidic oxygen during hydrolysis, another paper [4] suggested that Glu94, which is conserved among family-1, 2, 5, 10 and 17, might play a role as the general acid.
On the other hand, It is not clear which type of mechanisms is adopted by this enzyme, SN1 like mechanism or SN2-like reaction. The paper [5] suggested an SN2 mechanism, in which Glu231 serve as a nucleophile, attacking the anomeric carbon to generate a covalent-bonded intermediate.
Moreover, whether this enzyme adopts a retention mechanism, or an inversion one, is still unknown [6].
However, considering the other family-17 enzyme, Lichenase (E.C. 3.2.1.72) (S00209 in EzCatDB), the mechanism must be similar to that. Furthermore, comparing the structural data with that of xylanase (E.C. 3.2.1.8) (D00479 in EzCatDB), Tyr168 might stabilize the leaving nucleophile, Glu231 in deglycosylation. On the other hand, Tyr168 might modulate the activity of the nucleophile, according to the data of the other homologous enzyme, beta-glucosidase (E.C. 3.2.1.21) (S00205 in EzCatDB).

createdupdated
2003-02-032009-02-26


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 2010)
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)

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