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
27667
PubChem 22247451
962
439353
1gowA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1gowB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1qvbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1qvbB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 150;GLU 206;TYR 322;GLU 387
1gowB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 150;GLU 206;TYR 322;GLU 387
1qvbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 151;GLU 208;TYR 321;GLU 386
1qvbB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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).

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