DB code: S00206

RLCP classification	1.30.36200.973 : Hydrolysis
CATH domain	3.20.20.80 : TIM Barrel	Catalytic domain
E.C.	3.2.1.23
CSA
M-CSA
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 S00207 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

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	CAZy	Pfam
P22498	Beta-galactosidase	Lactase EC 3.2.1.23	NP_344331.1 (Protein) NC_002754.1 (DNA/RNA sequence)	GH1 (Glycoside Hydrolase Family 1)	PF00232 (Glyco_hydro_1) [Graphical View]
Q9YGA8		Beta-glycosidase		GH1 (Glycoside Hydrolase Family 1)	PF00232 (Glyco_hydro_1) [Graphical View]

KEGG enzyme name
beta-galactosidase lactase (ambiguous) beta-lactosidase maxilact hydrolact beta-D-lactosidase S 2107 lactozym trilactase beta-D-galactanase oryzatym sumiklat

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P22498	BGAL_SULSO	Hydrolysis of terminal non-reducing beta-D- galactose residues in beta-D-galactosides.	Homotetramer.
Q9YGA8	Q9YGA8_9CREN

KEGG Pathways
Map code	Pathways	E.C.
MAP00052	Galactose metabolism
MAP00511	N-Glycan degradation
MAP00531	Glycosaminoglycan degradation
MAP00561	Glycerolipid metabolism
MAP00600	Sphingolipid metabolism
MAP00604	Glycosphingolipid biosynthesis - ganglioseries
MAP01032	Glycan structures - degradation

Compound table
	Substrates		Products		Intermediates
KEGG-id	C00602	C00001	C00962	C00602
E.C.
Compound	beta-D-Galactoside	H2O	beta-D-Galactose	beta-D-Galactoside
Type	carbohydrate	H2O	carbohydrate	carbohydrate
ChEBI		15377 15377	27667 27667
PubChem		22247451 962 22247451 962	439353 439353

1gowA	Unbound		Unbound	Unbound
1gowB	Unbound		Unbound	Unbound
1qvbA	Unbound		Unbound	Unbound
1qvbB	Unbound		Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.
literature [2] & [3] (see [Comments])

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

1gowA	HIS 150;GLU 206;TYR 322;GLU 387
1gowB	HIS 150;GLU 206;TYR 322;GLU 387
1qvbA	HIS 151;GLU 208;TYR 321;GLU 386
1qvbB	HIS 151;GLU 208;TYR 321;GLU 386

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[3]	p.796-797
[4]	Fig.2, p.648-649	4
[5]	p.377-378

References
[1]
Resource
Comments
Medline ID
PubMed ID	7729513
Journal	FEBS Lett
Year	1995
Volume	362
Pages	281-5
Authors	Jenkins J, Lo Leggio L, Harris G, Pickersgill R
Title	Beta-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
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID	9010932
Journal	Protein Eng
Year	1996
Volume	9
Pages	1191-5
Authors	Moracci M, Capalbo L, Ciaramella M, Rossi M
Title	Identification of two glutamic acid residues essential for catalysis in the beta-glycosidase from the thermoacidophilic archaeon Sulfolobus solfataricus.
Related PDB
Related UniProtKB
[3]
Resource
Comments	X-ray crystallography (2.6 angstroms).
Medline ID	97446327
PubMed ID	9299327
Journal	J Mol Biol
Year	1997
Volume	271
Pages	789-802
Authors	Aguilar CF, Sanderson I, Moracci M, Ciaramella M, Nucci R, Rossi M, Pearl LH
Title	Crystal structure of the beta-glycosidase from the hyperthermophilic archeon Sulfolobus solfataricus: resilience as a key factor in thermostability.
Related PDB	1gow
Related UniProtKB	P22498
[4]
Resource
Comments
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
[5]
Resource
Comments
Medline ID
PubMed ID	10094493
Journal	FEBS Lett
Year	1999
Volume	445
Pages	375-83
Authors	Chi YI, Martinez-Cruz LA, Jancarik J, Swanson RV, Robertson DE, Kim SH
Title	Crystal structure of the beta-glycosidase from the hyperthermophile Thermosphaera aggregans: insights into its activity and thermostability.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	11749955
Journal	FEBS Lett
Year	2001
Volume	509
Pages	355-60
Authors	Corbett K, Fordham-Skelton AP, Gatehouse JA, Davis BG
Title	Tailoring the substrate specificity of the beta-glycosidase from the thermophilic archaeon Sulfolobus solfataricus.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the family-1 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 [1]. The liteature [2],[3] mentioned that the conserved glucamic acid residue at C-terminal end of beta-7 (Glu387 of 1gow) is the catalytic nucleophile, whilst another conserved residue at C-terminal end of beta-4 (Glu206) might function as a general acid in the first step, in which the covalent intermediate would be formed between the nucleophilic residue and the substrate, and as a general base for a nearby water in the second step, where the intermediate will be hydrolyzed by this water. However, the paper [3] suggested that a conserved histidine residue (His150) at beta-3 might play a role as the general base in the second step, by activating the water, although this residue is not conserved among all the families of 4/7-superfamily. The literature [4] 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 (Glu387 in 1gow) 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 (Glu206 or His150 in 1gow) 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 family-10 enzyme, xylanase (E.C. 3.2.1.8) (D00479 in EzCatDB), Tyr322 (of 1gow) might stabilize the leaving nucleophile, Glu387 in deglycosylation. On the other hand, Tyr322 might modulate the activity of the nucleophile, according to the data of the other family enzyme, beta-glucosidase (E.C. 3.2.1.21) (S00205 in EzCatDB).

Comments

This enzyme belongs to the family-1 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 [1].
The liteature [2],[3] mentioned that the conserved glucamic acid residue at C-terminal end of beta-7 (Glu387 of 1gow) is the catalytic nucleophile, whilst another conserved residue at C-terminal end of beta-4 (Glu206) might function as a general acid in the first step, in which the covalent intermediate would be formed between the nucleophilic residue and the substrate, and as a general base for a nearby water in the second step, where the intermediate will be hydrolyzed by this water. However, the paper [3] suggested that a conserved histidine residue (His150) at beta-3 might play a role as the general base in the second step, by activating the water, although this residue is not conserved among all the families of 4/7-superfamily.
The literature [4] 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 (Glu387 in 1gow) 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 (Glu206 or His150 in 1gow) 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 family-10 enzyme, xylanase (E.C. 3.2.1.8) (D00479 in EzCatDB), Tyr322 (of 1gow) might stabilize the leaving nucleophile, Glu387 in deglycosylation. On the other hand, Tyr322 might modulate the activity of the nucleophile, according to the data of the other family enzyme, beta-glucosidase (E.C. 3.2.1.21) (S00205 in EzCatDB).

Created	Updated
2003-02-03	2009-03-11