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 15377			4141 4141
PubChem	22247451 962 22247451 962			439404 439404

1pbgA		Unbound	Unbound	Unbound
1pbgB		Unbound	Unbound	Unbound
2pbgA		Unbound	Unbound	Unbound
3pbgA		Unbound	Unbound	Unbound
3pbgB		Unbound	Unbound	Unbound
4pbgA		Unbound	Unbound	Bound:BGP
4pbgB		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	GLU 160;TYR 299;GLU 375
1pbgB	GLU 160;TYR 299;GLU 375
2pbgA	GLU 160;TYR 299;GLU 375				mutant S256C
3pbgA	GLU 160;TYR 299;GLU 375
3pbgB	GLU 160;TYR 299;GLU 375
4pbgA	GLU 160;TYR 299;				mutant G375C
4pbgB	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).

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