EzCatDB: D00863
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DB codeD00863
RLCP classification1.30.35890.994 : Hydrolysis
CATH domainDomain 13.20.20.70 : TIM BarrelCatalytic domain
Domain 22.60.40.1180 : Immunoglobulin-like
E.C.3.2.1.22

CATH domainRelated DB codes (homologues)
2.60.40.1180 : Immunoglobulin-likeM00113,T00307,D00165,D00176,D00664,D00665,D00864,M00112,M00193,M00314,T00057,T00062,T00067
3.20.20.70 : TIM BarrelS00215,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,D00664,D00665,D00804,T00089

Enzyme Name
UniProtKBKEGG

Q02402
Protein name
Alpha-galactosidase
Melibiase
Alpha-D-galactosidase
Alpha-galactosidase A
Alpha-galactoside galactohydrolase
SynonymsAlpha-galactosidase
PfamPF02065 (Melibiase)
[Graphical view]
CAZyGH27 (Glycoside Hydrolase Family)

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

UniProtKB:Accession NumberQ02402
Entry nameQ02402_9FUNG
Activity
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC00883C00001C00984C02492I00062
CompoundgalactomannanH2Oalpha-D-Galactose1,4-beta-D-MannanPeptidyl-ASP-beta-D-galactose
TypepolysaccharideH2Ocarbohydratepolysaccharide
ChEBI27680
15377
28061


PubChem439336
962
22247451
439357


             
3a5vA01Unbound UnboundUnboundUnbound
3a5vA02Unbound UnboundUnboundUnbound

Active-site residues
resource
Literature [3], [4], [5], [6], [7], [8], [9] & Swiss-prot;P06280, Q9FXT4
pdbCatalytic residues
         
3a5vA01ASP 51;TYR  93;ASP 129;ARG 185;ASP 189
3a5vA02 

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 UniProtKBQ9FXT4
[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 UniProtKBP06280
[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 UniProtKBQ92456
[7]
JournalBiocatal Biotransformation
Year2009
Volume27
Pages79-89
AuthorsWeignerova' L, Simerska' P, Kr(en V
Titleƒ¿-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 UniProtKBP06280
[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 UniProtKBP06280

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 other organisms (EC 3.2.1.22; D00664), which shows different substrate specificities from this enzyme. This enzyme is specific only for galactomannan, whereas the counterpart enzyme is also active toward other alpha-galactosides (see [9]).
However, considering the conservation of the active-site structure, this enzyme must catalyze the same reaction type as these homologous enzymes.
Asp129 acts as a nucleophile, whereas Asp189 acts as catalytic acid-base.

createdupdated
2010-03-052012-02-01
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 2008)
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)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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