DB code: S00211

RLCP classification 1.30.36210.971 : Hydrolysis
CATH domain 3.20.20.80 : TIM Barrel Catalytic domain
E.C. 3.2.1.85
CSA 1pbg
M-CSA 1pbg
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 S00209 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
P11546 6-phospho-beta-galactosidase
EC 3.2.1.85
Beta-D-phosphogalactoside galactohydrolase
PGALase
P-beta-Gal
PBG
GH1 (Glycoside Hydrolase Family 1)
PF00232 (Glyco_hydro_1)
[Graphical View]

KEGG enzyme name
6-phospho-beta-galactosidase
phospho-beta-galactosidase
beta-D-phosphogalactoside galactohydrolase
phospho-beta-D-galactosidase
6-phospho-beta-D-galactosidase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P11546 LACG_LACLA A 6-phospho-beta-D-galactoside + H(2)O = 6- phospho-D-galactose + an alcohol.

KEGG Pathways
Map code Pathways E.C.
MAP00052 Galactose metabolism

Compound table
Substrates Products Intermediates
KEGG-id C00001 C03847 C00069 C01113
E.C.
Compound H2O 6-Phospho-beta-D-galactoside Alcohol D-Galactose 6-phosphate
Type H2O carbohydrate,phosphate group/phosphate ion carbohydrate carbohydrate,phosphate group/phosphate ion
ChEBI 15377
4141
PubChem 22247451
962
439404
1pbgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1pbgB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
2pbgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3pbgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
3pbgB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
4pbgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:BGP
4pbgB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:BGP

Reference for Active-site residues
resource references E.C.
PDB;3pbg & Swiss-prot;P11546

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1pbgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 160;TYR 299;GLU 375
1pbgB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 160;TYR 299;GLU 375
2pbgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 160;TYR 299;GLU 375 mutant S256C
3pbgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 160;TYR 299;GLU 375
3pbgB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 160;TYR 299;GLU 375
4pbgA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 160;TYR 299; mutant G375C
4pbgB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 160;TYR 299; mutant G375C

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[6]
p.964-965
[7]
p.855-857

References
[1]
Resource
Comments
Medline ID
PubMed ID 2125052
Journal J Biol Chem
Year 1990
Volume 265
Pages 22554-60
Authors de Vos WM, Boerrigter I, van Rooyen RJ, Reiche B, Hengstenberg W
Title Characterization of the lactose-specific enzymes of the phosphotransferase system in Lactococcus lactis.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 8398213
Journal FEMS Microbiol Rev
Year 1993
Volume 12
Pages 149-63
Authors Hengstenberg W, Kohlbrecher D, Witt E, Kruse R, Christiansen I, Peters D, Pogge von Strandmann R, Stadtler P, Koch B, Kalbitzer HR
Title Structure and function of proteins of the phosphotransferase system and of 6-phospho-beta-glycosidases in gram-positive bacteria.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7556220
Journal Eur J Biochem
Year 1995
Volume 232
Pages 658-63
Authors Staedtler P, Hoenig S, Frank R, Withers SG, Hengstenberg W
Title Identification of the active-site nucleophile in 6-phospho-beta-galactosidase from Staphylococcus aureus by labelling with synthetic inhibitors.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 8710837
Journal Proteins
Year 1995
Volume 23
Pages 446-53
Authors Benner SA, Gerloff D, Chelvanayagam G
Title The phospho-beta-galactosidase and synaptotagmin predictions.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 7567950
Journal Proteins
Year 1995
Volume 21
Pages 273-81
Authors Gerloff DL, Benner SA
Title A consensus prediction of the secondary structure for the 6-phospho-beta-D-galactosidase superfamily.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 96097402
PubMed ID 8535789
Journal Structure
Year 1995
Volume 3
Pages 961-8
Authors Wiesmann C, Beste G, Hengstenberg W, Schulz GE
Title The three-dimensional structure of 6-phospho-beta-galactosidase from Lactococcus lactis.
Related PDB 1pbg
Related UniProtKB P11546
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID 97366816
PubMed ID 9223646
Journal J Mol Biol
Year 1997
Volume 269
Pages 851-60
Authors Wiesmann C, Hengstenberg W, Schulz GE
Title Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis.
Related PDB 2pbg 3pbg 4pbg
Related UniProtKB P11546
[8]
Resource
Comments
Medline ID
PubMed ID 10906347
Journal Protein Eng
Year 2000
Volume 13
Pages 515-8
Authors Schulte D, Hengstenberg W
Title Engineering the active center of the 6-phospho-beta-galactosidase from Lactococcus lactis.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 14526081
Journal Science
Year 2003
Volume 302
Pages 106-9
Authors Ringler P, Schulz GE
Title Self-assembly of proteins into designed networks.
Related PDB
Related UniProtKB

Comments
This family belongs to glycosidase family-1, which has a retaining mechanism (equatorial to equatorial conformation), and also a family of 4/7 superfamily, which has got catalytic residues at the C-terminal ends of beta-4 and beta-7 on the (alpha/beta)8 barrel fold. The mechanism must be similar to those of 4/7 superfamily enzymes (such as S00203 in EzCatDB).
According to the literature [7], Glu375 and Glu160 act as a nucleophile and acid-base, respectively. The catalytic reaction is initiated by the protonation of Glu160 to the O1 atom of Gal-6P substrate. This suggests that the reaction proceeds through a dissociative-type (or SN1-like) mechanism, with a formation of oxocarbonium ion in the transition state, during the glycosylation of the active site. During the glycosylation, Glu375 makes a covalent bond with the C1 atom of the substrate.
At the second stage, or during the deglycosylation, a water molecule can be activated by a general base, Glu160.
Moreover, comparing the structural data with that of family-10 enzyme, xylanase (E.C. 3.2.1.8) (D00479 in EzCatDB), Tyr299 might stabilize the leaving nucleophile, Glu375 in deglycosylation. On the other hand, Tyr299 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
2004-05-25 2009-02-26