EzCatDB: D00664

DB codeD00664
RLCP classification1.30.35890.994
CATH domainDomain 13.20.20.70Catalytic domain
Domain 22.60.40.1180
E.C.3.2.1.22
CSA1uas

CATH domainRelated DB codes (homologues)
2.60.40.1180M00113,T00307,D00165,D00176,D00665,D00863,D00864,M00112,M00193,M00314,T00057,T00062,T00067
3.20.20.70S00215,S00217,S00218,S00219,S00532,S00198,S00220,S00745,S00537,S00538,S00539,S00826,S00841,S00235,S00239,S00240,S00243,S00244,S00199,S00200,S00201,S00221,S00222,S00847,S00224,S00225,S00226,D00014,D00029,M00141,T00015,T00239,D00665,D00804,D00863,T00089

Enzyme Name
Swiss-protKEGG

Q92456Q9FXT4P06280
Protein name
Alpha-galactosidaseAlpha-galactosidase A (EC 3.2.1.22) (Alpha-D-galactoside galactohydrolase) (Alpha-D-galactosidase A) (Melibiase)AltName: INN=Agalsidase;Alpha-galactosidase
Melibiase
Alpha-D-galactosidase
Alpha-galactosidase A
Alpha-galactoside galactohydrolase
SynonymsAlpha-galactosidase
EC 3.2.1.22
EC 3.2.1.22
Alpha-D-galactoside galactohydrolase
Melibiase
None

KEGG pathways
MAP codePathways
MAP00052Galactose metabolism
MAP00561Glycerolipid metabolism
MAP00600Sphingolipid metabolism
MAP00603Glycosphingolipid biosynthesis - globoseries

Swiss-prot:Accession NumberQ92456Q9FXT4P06280
Entry nameQ92456_HYPJEAGAL_ORYSAAGAL_HUMAN
Activity
Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase.Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase.
Subunit

Homodimer.
Subcellular location

Lysosome.
Cofactor




SubstratesProductsintermediates
KEGG-idL00045C05402C00883C00001C00984L00045C00031C02492I00062
Compoundalpha-D-galactosideMelibiosegalactomannanH2Oalpha-D-Galactosealpha-D-galactosideD-Glucose1,4-beta-D-MannanPeptidyl-ASP-beta-D-galactose
TypepolysaccharidepolysaccharidepolysaccharideH2Ocarbohydratepolysaccharidecarbohydratepolysaccharide
1sznA01UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
1t0oA01UnboundUnboundUnbound
Analogue:GALUnboundUnboundUnboundUnbound
1uasA01UnboundUnboundUnbound
Bound:GLAUnboundUnboundUnboundUnbound
1r46A01UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
1r46B01UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
1r47A01UnboundUnboundUnbound
Analogue:GALUnboundUnboundUnboundUnbound
1r47B01UnboundUnboundUnbound
Analogue:GALUnboundUnboundUnboundUnbound
3gxnA01UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3gxnB01UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3gxpA01UnboundUnboundUnbound
Bound:GLAUnboundUnboundUnboundUnbound
3gxpB01UnboundUnboundUnbound
Bound:GLAUnboundUnboundUnboundUnbound
3gxtA01UnboundUnboundUnbound
Analogue:NOJUnboundUnboundUnboundUnbound
3gxtB01UnboundUnboundUnbound
Analogue:NOJUnboundUnboundUnboundUnbound
3hg2A01UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3hg2B01UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3hg3A01UnboundBound:GLA-GLCUnbound
UnboundUnboundUnboundUnboundUnbound
3hg3B01UnboundBound:GLA-GLCUnbound
UnboundUnboundUnboundUnboundUnbound
3hg4A01UnboundUnboundUnbound
UnboundUnboundUnboundUnboundIntermediate-analogue:7JZ
3hg4B01UnboundUnboundUnbound
UnboundUnboundUnboundUnboundIntermediate-analogue:7JZ
3hg5A01UnboundUnboundUnbound
Bound:GLAUnboundUnboundUnboundUnbound
3hg5B01UnboundUnboundUnbound
Bound:GLAUnboundUnboundUnboundUnbound
1sznA02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
1t0oA02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
1uasA02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
1r46A02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
1r46B02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
1r47A02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
1r47B02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3gxnA02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3gxnB02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3gxpA02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3gxpB02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3gxtA02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3gxtB02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3hg2A02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3hg2B02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3hg3A02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3hg3B02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3hg4A02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3hg4B02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3hg5A02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound
3hg5B02UnboundUnboundUnbound
UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Literature [3], [4], [5], [6], [7], [8], [9] & Swiss-prot;P06280, Q9FXT4
pdbCatalytic residuescomment
1sznA01ASP 54;TYR  96;ASP 132;ARG 222;ASP 226

1t0oA01ASP 54;TYR  96;ASP 132;ARG 222;ASP 226

1uasA01ASP 51;TYR  93;ASP 130;ARG 181;ASP 185

1r46A01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

1r46B01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

1r47A01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

1r47B01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3gxnA01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3gxnB01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3gxpA01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3gxpB01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3gxtA01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3gxtB01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3hg2A01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3hg2B01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3hg3A01ASP 92;TYR 134;       ;ARG 227;ASP 231
mutant D170A
3hg3B01ASP 92;TYR 134;       ;ARG 227;ASP 231
mutant D170A
3hg4A01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3hg4B01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3hg5A01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

3hg5B01ASP 92;TYR 134;ASP 170;ARG 227;ASP 231

1sznA02

1t0oA02

1uasA02

1r46A02

1r46B02

1r47A02

1r47B02

3gxnA02

3gxnB02

3gxpA02

3gxpB02

3gxtA02

3gxtB02

3hg2A02

3hg2B02

3hg3A02

3hg3B02

3hg4A02

3hg4B02

3hg5A02

3hg5B02


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]Figure 4
[6]p.417-419
[9]FIGURE 1
[10]Fig.2, Fig.3, p.3627-3630

references
[1]
PubMed ID10933800
JournalBiochemistry
Year2000
Volume39
Pages9826-36
AuthorsHart DO, He S, Chany CJ 2nd, Withers SG, Sims PF, Sinnott ML, Brumer H 3rd
TitleIdentification of Asp-130 as the catalytic nucleophile in the main alpha-galactosidase from Phanerochaete chrysosporium, a family 27 glycosyl hydrolase.
[2]
PubMed ID11128583
JournalCarbohydr Res
Year2000
Volume329
Pages539-47
AuthorsLy HD, Howard S, Shum K, He S, Zhu A, Withers SG
TitleThe synthesis, testing and use of 5-fluoro-alpha-D-galactosyl fluoride to trap an intermediate on green coffee bean alpha-galactosidase and identify the catalytic nucleophile.
[3]
PubMed ID12005440
JournalStructure
Year2002
Volume10
Pages425-34
AuthorsGarman SC, Hannick L, Zhu A, Garboczi DN
TitleThe 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 56-417 IN COMPLEX WITH D-GALACTOSE.
PubMed ID12657636
JournalJ Biol Chem
Year2003
Volume278
Pages20313-8
AuthorsFujimoto Z, Kaneko S, Momma M, Kobayashi H, Mizuno H
TitleCrystal structure of rice alpha-galactosidase complexed with D-galactose.
Related PDB1uas
Related Swiss-protQ9FXT4
[5]
CommentsX-RAY CRYSTALLOGRAPHY (3.45 ANGSTROMS) OF 32-422 IN COMPLEX WITH PRODUCT, HOMODIMERIZATION, GLYCOSYLATION AT ASN-139; ASN-192 AND ASN-215.
PubMed ID15003450
JournalJ Mol Biol
Year2004
Volume337
Pages319-35
AuthorsGarman SC, Garboczi DN
TitleThe molecular defect leading to Fabry disease: structure of human alpha-galactosidase.
Related PDB1r46,1r47
Related Swiss-protP06280
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.54 ANGSTROMS) OF 28-441.
PubMed ID15136043
JournalJ Mol Biol
Year2004
Volume339
Pages413-22
AuthorsGolubev AM, Nagem RA, Brandao Neto JR, Neustroev KN, Eneyskaya EV, Kulminskaya AA, Shabalin KA, Savel'ev AN, Polikarpov I
TitleCrystal structure of alpha-galactosidase from Trichoderma reesei and its complex with galactose: implications for catalytic mechanism.
Related PDB1szn,1t0o
Related Swiss-protQ92456
[7]
JournalBiocatal Biotransformation
Year2009
Volume27
Pages79-89
AuthorsWeignerova' L, Simerska' P, Kr(en V
Title??-Galactosidases and their applications in biotransformations.
[8]
PubMed ID19374450
JournalBiochemistry
Year2009
Volume48
Pages4816-27
AuthorsLieberman RL, D'aquino JA, Ringe D, Petsko GA
TitleEffects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability.
Related PDB3gxn,3gxp,3gxt
Related Swiss-protP06280
[9]
PubMed ID19809163
JournalBiosci Biotechnol Biochem
Year2009
Volume73
Pages2360-4
AuthorsFujimoto Z, Kaneko S, Kim WD, Park GG, Momma M, Kobayashi H
TitleThe tetramer structure of the glycoside hydrolase family 27 alpha-galactosidase I from Umbelopsis vinacea.
Related PDB3a5v
[10]
PubMed ID19940122
JournalJ Biol Chem
Year2010
Volume285
Pages3625-32
AuthorsGuce AI, Clark NE, Salgado EN, Ivanen DR, Kulminskaya AA, Brumer H 3rd, Garman SC
TitleCatalytic mechanism of human alpha-galactosidase.
Related PDB3hg2,3hg3,3hg4,3hg5
Related Swiss-protP06280

comments
This enzyme belongs to glycosidase family-27, with a retaining mechanism.
Alpha-galactosidases can be classified into glycosidase family-4, 27, 36, 57, 97 and 110 (see [9]). Alpha-galactosidases from eukaryotes are generally classified into glycosidase family-27, whereas prokaryotic alpha-galactosidases are mostly classified into glycosidase family-36 (see [9]).
This enzyme is homologous to alpha-N-acetylgalactosaminidase (EC 3.2.1.49; D00665 in EzCatDB) and a counterpart enzyme from fungi (EC 3.2.1.22; D00863), which is specific for galactomannan.
According to the literature [5], [6] and [10], the reaction proceeds as follows:
(0) Considering the conservation and relative location of active-site residues, Arg227 (of 1r46) modulates the activity of Asp231, whilst Tyr134 modulates the activity of Asp170.
(1) Asp231 (of 1r46) acts as a general acid to protonate the leaving group. This protonation may form an oxocarbenium-ion like transition-state. Asp92 may stabilize the transition-state through hydrogen bond with O4 atom of alpha-galactoside substrate.
(2) Meanwhile, Asp170 makes a nucleophilic attack on the C1 atom of alpha-D-galactoside at the non-reducing end, forming a covalent intermediate with an inverted configuration at C1. (SN1-like reaction)
(3) Asp231 acts as a general base to deprotonate a water molecule, to activate it.
(4) The activated water makes a nucleophilic attack on the C1 atom of the covalent intermediate, releasing the alpha-D-galactose product.

createdupdated
2010-03-052012-02-07
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)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.