DB code: D00664

RLCP classification 1.30.35890.994 : Hydrolysis
CATH domain 3.20.20.70 : TIM Barrel Catalytic domain
2.60.40.1180 : Immunoglobulin-like
E.C. 3.2.1.22
CSA 1uas
M-CSA 1uas
MACiE

CATH domain Related DB codes (homologues)
3.20.20.70 : TIM Barrel S00215 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
2.60.40.1180 : Immunoglobulin-like M00113 T00307 D00165 D00176 D00665 D00863 D00864 M00112 M00193 M00314 T00057 T00062 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam RefSeq
Q92456
Alpha-galactosidase
EC 3.2.1.22
GH27 (Glycoside Hydrolase Family 27)
PF02065 (Melibiase)
[Graphical View]
Q9FXT4 Alpha-galactosidase
EC 3.2.1.22
Alpha-D-galactoside galactohydrolase
Melibiase
GH27 (Glycoside Hydrolase Family 27)
PF02065 (Melibiase)
[Graphical View]
NP_001064939.2 (Protein)
NM_001071474.2 (DNA/RNA sequence)
P06280 Alpha-galactosidase A (EC 3.2.1.22) (Alpha-D-galactosidase A) (Alpha-D-galactoside galactohydrolase) (Melibiase)AltName: INN=Agalsidase;
None GH27 (Glycoside Hydrolase Family 27)
PF02065 (Melibiase)
[Graphical View]
NP_000160.1 (Protein)
NM_000169.2 (DNA/RNA sequence)

KEGG enzyme name
Alpha-galactosidase
Melibiase
Alpha-D-galactosidase
Alpha-galactosidase A
Alpha-galactoside galactohydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q92456 Q92456_HYPJE
Q9FXT4 AGAL_ORYSA Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase.
P06280 AGAL_HUMAN Hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase. Homodimer. Lysosome.

KEGG Pathways
Map code Pathways E.C.
MAP00052 Galactose metabolism
MAP00561 Glycerolipid metabolism
MAP00600 Sphingolipid metabolism
MAP00603 Glycosphingolipid biosynthesis - globoseries

Compound table
Substrates Products Intermediates
KEGG-id L00045 C05402 C00883 C00001 C00984 L00045 C00031 C02492 I00062
E.C.
Compound alpha-D-galactoside Melibiose galactomannan H2O alpha-D-Galactose alpha-D-galactoside D-Glucose 1,4-beta-D-Mannan Peptidyl-ASP-beta-D-galactose
Type polysaccharide polysaccharide polysaccharide H2O carbohydrate polysaccharide carbohydrate polysaccharide
ChEBI 28053
27680
15377
28061
4167
PubChem 440658
439336
22247451
962
439357
5793
1sznA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1t0oA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:GAL Unbound Unbound Unbound Unbound
1uasA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:GLA Unbound Unbound Unbound Unbound
1r46A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1r46B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1r47A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:GAL Unbound Unbound Unbound Unbound
1r47B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:GAL Unbound Unbound Unbound Unbound
3gxnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3gxnB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3gxpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:GLA Unbound Unbound Unbound Unbound
3gxpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:GLA Unbound Unbound Unbound Unbound
3gxtA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:NOJ Unbound Unbound Unbound Unbound
3gxtB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Analogue:NOJ Unbound Unbound Unbound Unbound
3hg2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3hg2B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3hg3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:GLA-GLC Unbound Unbound Unbound Unbound Unbound Unbound
3hg3B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:GLA-GLC Unbound Unbound Unbound Unbound Unbound Unbound
3hg4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:7JZ
3hg4B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Intermediate-analogue:7JZ
3hg5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:GLA Unbound Unbound Unbound Unbound
3hg5B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:GLA Unbound Unbound Unbound Unbound
1sznA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1t0oA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1uasA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1r46A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1r46B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1r47A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1r47B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3gxnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3gxnB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3gxpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3gxpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3gxtA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3gxtB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3hg2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3hg2B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3hg3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3hg3B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3hg4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3hg4B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3hg5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
3hg5B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Literature [3], [4], [5], [6], [7], [8], [9] & Swiss-prot;P06280, Q9FXT4

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1sznA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 54;TYR 96;ASP 132;ARG 222;ASP 226
1t0oA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 54;TYR 96;ASP 132;ARG 222;ASP 226
1uasA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 51;TYR 93;ASP 130;ARG 181;ASP 185
1r46A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
1r46B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
1r47A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
1r47B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3gxnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3gxnB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3gxpA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3gxpB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3gxtA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3gxtB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3hg2A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3hg2B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3hg3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;;ARG 227;ASP 231 mutant D170A
3hg3B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;;ARG 227;ASP 231 mutant D170A
3hg4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3hg4B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3hg5A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
3hg5B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 92;TYR 134;ASP 170;ARG 227;ASP 231
1sznA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1t0oA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1uasA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1r46A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1r46B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1r47A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1r47B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3gxnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3gxnB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3gxpA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3gxpB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3gxtA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3gxtB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3hg2A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3hg2B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3hg3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3hg3B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3hg4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3hg4B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3hg5A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3hg5B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
Figure 4
[6]
p.417-419
[9]
FIGURE 1
[10]
Fig.2, Fig.3, p.3627-3630

References
[1]
Resource
Comments
Medline ID
PubMed ID 10933800
Journal Biochemistry
Year 2000
Volume 39
Pages 9826-36
Authors Hart DO, He S, Chany CJ 2nd, Withers SG, Sims PF, Sinnott ML, Brumer H 3rd
Title Identification of Asp-130 as the catalytic nucleophile in the main alpha-galactosidase from Phanerochaete chrysosporium, a family 27 glycosyl hydrolase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 11128583
Journal Carbohydr Res
Year 2000
Volume 329
Pages 539-47
Authors Ly HD, Howard S, Shum K, He S, Zhu A, Withers SG
Title The 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.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 12005440
Journal Structure
Year 2002
Volume 10
Pages 425-34
Authors Garman SC, Hannick L, Zhu A, Garboczi DN
Title The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 56-417 IN COMPLEX WITH D-GALACTOSE.
Medline ID
PubMed ID 12657636
Journal J Biol Chem
Year 2003
Volume 278
Pages 20313-8
Authors Fujimoto Z, Kaneko S, Momma M, Kobayashi H, Mizuno H
Title Crystal structure of rice alpha-galactosidase complexed with D-galactose.
Related PDB 1uas
Related UniProtKB Q9FXT4
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.45 ANGSTROMS) OF 32-422 IN COMPLEX WITH PRODUCT, HOMODIMERIZATION, GLYCOSYLATION AT ASN-139; ASN-192 AND ASN-215.
Medline ID
PubMed ID 15003450
Journal J Mol Biol
Year 2004
Volume 337
Pages 319-35
Authors Garman SC, Garboczi DN
Title The molecular defect leading to Fabry disease: structure of human alpha-galactosidase.
Related PDB 1r46 1r47
Related UniProtKB P06280
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.54 ANGSTROMS) OF 28-441.
Medline ID
PubMed ID 15136043
Journal J Mol Biol
Year 2004
Volume 339
Pages 413-22
Authors Golubev AM, Nagem RA, Brandao Neto JR, Neustroev KN, Eneyskaya EV, Kulminskaya AA, Shabalin KA, Savel'ev AN, Polikarpov I
Title Crystal structure of alpha-galactosidase from Trichoderma reesei and its complex with galactose: implications for catalytic mechanism.
Related PDB 1szn 1t0o
Related UniProtKB Q92456
[7]
Resource
Comments
Medline ID
PubMed ID
Journal Biocatal Biotransformation
Year 2009
Volume 27
Pages 79-89
Authors Weignerova' L, Simerska' P, Kr(en V
Title alpha-Galactosidases and their applications in biotransformations.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 19374450
Journal Biochemistry
Year 2009
Volume 48
Pages 4816-27
Authors Lieberman RL, D'aquino JA, Ringe D, Petsko GA
Title Effects of pH and iminosugar pharmacological chaperones on lysosomal glycosidase structure and stability.
Related PDB 3gxn 3gxp 3gxt
Related UniProtKB P06280
[9]
Resource
Comments
Medline ID
PubMed ID 19809163
Journal Biosci Biotechnol Biochem
Year 2009
Volume 73
Pages 2360-4
Authors Fujimoto Z, Kaneko S, Kim WD, Park GG, Momma M, Kobayashi H
Title The tetramer structure of the glycoside hydrolase family 27 alpha-galactosidase I from Umbelopsis vinacea.
Related PDB 3a5v
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 19940122
Journal J Biol Chem
Year 2010
Volume 285
Pages 3625-32
Authors Guce AI, Clark NE, Salgado EN, Ivanen DR, Kulminskaya AA, Brumer H 3rd, Garman SC
Title Catalytic mechanism of human alpha-galactosidase.
Related PDB 3hg2 3hg3 3hg4 3hg5
Related UniProtKB P06280

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.

Created Updated
2010-03-05 2018-04-23