EzCatDB: S00211

DB codeS00211
RLCP classification1.30.36210.971
CATH domainDomain 13.20.20.80Catalytic domain
E.C.3.2.1.85
CSA1pbg

CATH domainRelated DB codes (homologues)
3.20.20.80S00202,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

Enzyme Name
Swiss-protKEGG

P11546
Protein name6-phospho-beta-galactosidase6-phospho-beta-galactosidase
phospho-beta-galactosidase
beta-D-phosphogalactoside galactohydrolase
phospho-beta-D-galactosidase
6-phospho-beta-D-galactosidase
SynonymsEC 3.2.1.85
Beta-D-phosphogalactoside galactohydrolase
PGALase
P-beta-Gal
PBG

KEGG pathways
MAP codePathways
MAP00052Galactose metabolism

Swiss-prot:Accession NumberP11546
Entry nameLACG_LACLA
ActivityA 6-phospho-beta-D-galactoside + H(2)O = 6- phospho-D-galactose + an alcohol.
Subunit
Subcellular location
Cofactor


SubstratesProducts
KEGG-idC00001C03847C00069C01113
CompoundH2O6-Phospho-beta-D-galactosideAlcoholD-Galactose 6-phosphate
TypeH2Ocarbohydrate,phosphate group/phosphate ioncarbohydratecarbohydrate,phosphate group/phosphate ion
1pbgA
UnboundUnboundUnbound
1pbgB
UnboundUnboundUnbound
2pbgA
UnboundUnboundUnbound
3pbgA
UnboundUnboundUnbound
3pbgB
UnboundUnboundUnbound
4pbgA
UnboundUnboundBound:BGP
4pbgB
UnboundUnboundBound:BGP

Active-site residues
resource
PDB;3pbg & Swiss-prot;P11546
pdbCatalytic residuescomment
1pbgAGLU 160;TYR 299;GLU 375

1pbgBGLU 160;TYR 299;GLU 375

2pbgAGLU 160;TYR 299;GLU 375
mutant S256C
3pbgAGLU 160;TYR 299;GLU 375

3pbgBGLU 160;TYR 299;GLU 375

4pbgAGLU 160;TYR 299;       
mutant G375C
4pbgBGLU 160;TYR 299;       
mutant G375C

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[6]p.964-965
[7]p.855-857

references
[1]
PubMed ID2125052
JournalJ Biol Chem
Year1990
Volume265
Pages22554-60
Authorsde Vos WM, Boerrigter I, van Rooyen RJ, Reiche B, Hengstenberg W
TitleCharacterization of the lactose-specific enzymes of the phosphotransferase system in Lactococcus lactis.
[2]
PubMed ID8398213
JournalFEMS Microbiol Rev
Year1993
Volume12
Pages149-63
AuthorsHengstenberg W, Kohlbrecher D, Witt E, Kruse R, Christiansen I, Peters D, Pogge von Strandmann R, Stadtler P, Koch B, Kalbitzer HR
TitleStructure and function of proteins of the phosphotransferase system and of 6-phospho-beta-glycosidases in gram-positive bacteria.
[3]
PubMed ID7556220
JournalEur J Biochem
Year1995
Volume232
Pages658-63
AuthorsStaedtler P, Hoenig S, Frank R, Withers SG, Hengstenberg W
TitleIdentification of the active-site nucleophile in 6-phospho-beta-galactosidase from Staphylococcus aureus by labelling with synthetic inhibitors.
[4]
PubMed ID8710837
JournalProteins
Year1995
Volume23
Pages446-53
AuthorsBenner SA, Gerloff D, Chelvanayagam G
TitleThe phospho-beta-galactosidase and synaptotagmin predictions.
[5]
PubMed ID7567950
JournalProteins
Year1995
Volume21
Pages273-81
AuthorsGerloff DL, Benner SA
TitleA consensus prediction of the secondary structure for the 6-phospho-beta-D-galactosidase superfamily.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID96097402
PubMed ID8535789
JournalStructure
Year1995
Volume3
Pages961-8
AuthorsWiesmann C, Beste G, Hengstenberg W, Schulz GE
TitleThe three-dimensional structure of 6-phospho-beta-galactosidase from Lactococcus lactis.
Related PDB1pbg
Related Swiss-protP11546
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID97366816
PubMed ID9223646
JournalJ Mol Biol
Year1997
Volume269
Pages851-60
AuthorsWiesmann C, Hengstenberg W, Schulz GE
TitleCrystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis.
Related PDB2pbg,3pbg,4pbg
Related Swiss-protP11546
[8]
PubMed ID10906347
JournalProtein Eng
Year2000
Volume13
Pages515-8
AuthorsSchulte D, Hengstenberg W
TitleEngineering the active center of the 6-phospho-beta-galactosidase from Lactococcus lactis.
[9]
PubMed ID14526081
JournalScience
Year2003
Volume302
Pages106-9
AuthorsRingler P, Schulz GE
TitleSelf-assembly of proteins into designed networks.

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).

createdupdated
2004-05-252009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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