EzCatDB: S00209

DB codeS00209
RLCP classification1.30.36210.971
CATH domainDomain 13.20.20.80Catalytic domain
E.C.3.2.1.73
CSA1aq0

CATH domainRelated DB codes (homologues)
3.20.20.80S00202,S00210,S00748,S00906,S00907,S00911,S00912,S00915,M00134,M00160,D00479,S00204,S00205,S00206,S00207,S00203,S00208,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

P12257
Protein nameLichenase-2licheninase
lichenase
beta-(1->4)-D-glucan 4-glucanohydrolase
1,3
1,4-beta-glucan endohydrolase
1,3
1,4-beta-glucan 4-glucanohydrolase
1,3-1,4-beta-D-glucan 4-glucanohydrolase
SynonymsEC 3.2.1.73
Lichenase II
Endo-beta-1,3-1,4 glucanase II
Endo-beta-1,3-1,4 glucanase II) ((1->3,1->4)-beta-glucanase isoenzyme EII


Swiss-prot:Accession NumberP12257
Entry nameGUB2_HORVU
ActivityHydrolysis of (1->4)-beta-D-glucosidic linkages in beta-D-glucans containing (1->3)- and (1->4)-bonds.
Subunit
Subcellular location
Cofactor


SubstratesProducts
KEGG-idC00551C00001C00478C00551
Compoundbeta-D-GlucanH2OLicheninbeta-D-Glucan
TypepolysaccharideH2Ocarbohydratepolysaccharide
1aq0AUnbound
UnboundUnbound
1aq0BUnbound
UnboundUnbound
1ghrAUnbound
UnboundUnbound

Active-site residues
resource
see [Comments]
pdbCatalytic residues
1aq0AGLU 93;TYR 170;GLU 232
1aq0BGLU 93;TYR 170;GLU 232
1ghrAGLU 93;TYR 170;GLU 232

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[2]p.13322
[5]p.Fig.2, p.648-6504
[7]p.30108-30111

references
[1]
Commentscrystallization, preliminary X-ray diffraction 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 acids, evolution
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 (2.2 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 PDB1ghr
Related Swiss-protP12257
[4]
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.
[5]
CommentsReview
PubMed ID9345622
JournalCurr Opin Struct Biol
Year1997
Volume7
Pages645-51
AuthorsWhite A, Rose DR
TitleMechanism of catalysis by retaining beta-glycosyl hydrolases.
[6]
CommentsX-ray crystallography (2.0 angstroms).
Medline ID98123117
PubMed ID9452466
JournalJ Biol Chem
Year1998
Volume273
Pages3438-46
AuthorsMueller JJ, Thomsen KK, Heinemann U
TitleCrystal structure of barley 1,3-1,4-beta-glucanase at 2.0-A resolution and comparison with Bacillus 1,3-1,4-beta-glucanase.
Related PDB1aq0
Related Swiss-protP12257
[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.
Glu232 has been reported to be the nucleophilic residue of this enzyme [2]. This paper [2] also suggested that Glu288 is likely to be the catalytic acid. However, another paper [7] suggested that Glu94 is most likely to be the catalytic acid/base. Comparing with other 4/7 superfamily enzymes, Glu288 is too distant from the nucleophile, Glu232. Thus, Glu94 must be the acid/base.
The literature [5] described general aspects of the catalytic mechanism of retaining beta-glycosyl hydrolases. Accoriding to the paper, the mechanism can be described as follows:
(1) Saccharide binds in a "twisted-boat" conformation.
(2) The beta-1,4 linkage is broken, leading to the formation of a transition state with a slight positive charge at the anomeric carbon, in a "half-chair" conformation, which develops a oxocarbenium-ion-like character.
(3) An approach of the ionic species to the catalytic nucleophile leads to the formation of a covalent intermediate of inverted alpha-configuration in a so-called chair conformation. The aglycon is released and a water molecule diffuses into the vicinity of the acidic residue as a general base.
(4) The covalent intermediate reactivates through an oxocarbenium-ion-like transition state. The general base abstracts a proton from the incoming water, which in turn carries out a nucleophilic attack on the C1 atom of the residual saccharide.
Moreover, comparing the structural data with that of xylanase (E.C. 3.2.1.8) (D00479 in EzCatDB), Tyr170 might stabilize the leaving nucleophile, Glu232 in deglycosylation. On the other hand, Tyr170 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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