DB code: S00209

RLCP classification	1.30.36210.971 : Hydrolysis
CATH domain	3.20.20.80 : TIM Barrel	Catalytic domain
E.C.	3.2.1.73
CSA	1aq0
M-CSA	1aq0
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 S00211 S00213 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
P12257	Lichenase-2	EC 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	GH17 (Glycoside Hydrolase Family 17)	PF00332 (Glyco_hydro_17) [Graphical View]

KEGG enzyme name
licheninase 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

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P12257	GUB2_HORVU	Hydrolysis of (1->4)-beta-D-glucosidic linkages in beta-D-glucans containing (1->3)- and (1->4)-bonds.

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Substrates			Products	Intermediates
KEGG-id	C00551	C00001	C00478	C00551
E.C.
Compound	beta-D-Glucan	H2O	Lichenin	beta-D-Glucan
Type	polysaccharide	H2O	carbohydrate	polysaccharide
ChEBI		15377 15377
PubChem	46173706 46173706	22247451 962 22247451 962	439241 439241	46173706 46173706

1aq0A	Unbound		Unbound	Unbound
1aq0B	Unbound		Unbound	Unbound
1ghrA	Unbound		Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
see [Comments]

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1aq0A	GLU 93;TYR 170;GLU 232
1aq0B	GLU 93;TYR 170;GLU 232
1ghrA	GLU 93;TYR 170;GLU 232

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[2]	p.13322
[5]	p.Fig.2, p.648-650	4
[7]	p.30108-30111

References
[1]
Resource
Comments	crystallization, preliminary X-ray diffraction analysis (1.8 angstroms)
Medline ID
PubMed ID	8254681
Journal	J Mol Biol
Year	1993
Volume	234
Pages	888-9
Authors	Chen L, Garrett TJ, Varghese JN, Fincher GB, Hoj PB
Title	Crystallization and preliminary X-ray analysis of (1,3)- and (1,3;1,4)-beta-D-glucanases from germinating barley.
Related PDB
Related UniProtKB
[2]
Resource
Comments	catalytic amino acids, evolution
Medline ID
PubMed ID	8514770
Journal	J Biol Chem
Year	1993
Volume	268
Pages	13318-26
Authors	Chen L, Fincher GB, Hoj PB
Title	Evolution of polysaccharide hydrolase substrate specificity. Catalytic amino acids are conserved in barley 1,3-1,4- and 1,3-beta-glucanases.
Related PDB
Related UniProtKB
[3]
Resource
Comments	X-ray crystallography (2.2 angstroms).
Medline ID	94195828
PubMed ID	8146192
Journal	Proc Natl Acad Sci USA
Year	1994
Volume	91
Pages	2785-9
Authors	Varghese JN, Garrett TPJ, Colman PM, Chen L, Hoej PB, Fincher GB
Title	Three-dimensional structures of two plant beta-glucan endohydrolases with distinct substrate specificities.
Related PDB	1ghr
Related UniProtKB	P12257
[4]
Resource
Comments
Medline ID
PubMed ID	7492591
Journal	Biochim Biophys Acta
Year	1995
Volume	1253
Pages	112-6
Authors	Chen L, Sadek M, Stone BA, Brownlee RT, Fincher GB, Hoj PB
Title	Stereochemical course of glucan hydrolysis by barley (1-->3)- and (1-->3, 1-->4)-beta-glucanases.
Related PDB
Related UniProtKB
[5]
Resource
Comments	Review
Medline ID
PubMed ID	9345622
Journal	Curr Opin Struct Biol
Year	1997
Volume	7
Pages	645-51
Authors	White A, Rose DR
Title	Mechanism of catalysis by retaining beta-glycosyl hydrolases.
Related PDB
Related UniProtKB
[6]
Resource
Comments	X-ray crystallography (2.0 angstroms).
Medline ID	98123117
PubMed ID	9452466
Journal	J Biol Chem
Year	1998
Volume	273
Pages	3438-46
Authors	Mueller JJ, Thomsen KK, Heinemann U
Title	Crystal 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 PDB	1aq0
Related UniProtKB	P12257
[7]
Resource
Comments
Medline ID
PubMed ID	12023973
Journal	J Biol Chem
Year	2002
Volume	277
Pages	30102-11
Authors	Hrmova M, Imai T, Rutten SJ, Fairweather JK, Pelosi L, Bulone V, Driguez H, Fincher GB
Title	Mutated varley (1,3)-beta-D-glucan endohydrolases synthesize crystalline (1,3)-beta-D-glucans.
Related PDB
Related UniProtKB

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).

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).

Created	Updated
2003-02-03	2009-02-26