EzCatDB: D00665
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DB codeD00665
RLCP classification1.30.35890.994 : Hydrolysis
CATH domainDomain 13.20.20.70 : TIM BarrelCatalytic domain
Domain 22.60.40.1180 : Immunoglobulin-like
E.C.3.2.1.49

CATH domainRelated DB codes (homologues)
2.60.40.1180 : Immunoglobulin-likeM00113,T00307,D00165,D00176,D00664,D00863,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,D00804,D00863,T00089

Enzyme Name
UniProtKBKEGG

Q90744P17050
Protein nameAlpha-N-acetylgalactosaminidaseAlpha-N-acetylgalactosaminidaseAlpha-N-acetylgalactosaminidase
Alpha-acetylgalactosaminidase
N-acetyl-alpha-D-galactosaminidase
N-acetyl-alpha-galactosaminidase
SynonymsEC 3.2.1.49
Alpha-galactosidase B
EC 3.2.1.49
Alpha-galactosidase B
RefSeq
NP_000253.1 (Protein)
NM_000262.2 (DNA/RNA sequence)
PfamPF02065 (Melibiase)
[Graphical view]
PF02065 (Melibiase)
[Graphical view]
CAZyGH27 (Glycoside Hydrolase Family)
GH27 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00603Glycosphingolipid biosynthesis - globoseries

UniProtKB:Accession NumberQ90744P17050
Entry nameNAGAB_CHICKNAGAB_HUMAN
ActivityHydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D-galactosaminides.Hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D-galactosaminides.
SubunitHomodimer.Homodimer.
Subcellular locationLysosome (By similarity).Lysosome.
Cofactor


Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC04134C00001C04134L00046I00063
CompoundN-Acetyl-alpha-D-galactosaminideH2ON-Acetyl-alpha-D-galactosaminideN-Acetyl-alpha-D-galactosaminePeptidyl-ASP-beta-N-acetylgalactosaminie
Typeamide group,polysaccharideH2Oamide group,polysaccharideamide group,carbohydrate
ChEBI
15377

40356

PubChem
962
22247451

84265

             
1ktbA01Unbound UnboundUnboundUnbound
1ktcA01Unbound UnboundBound:NGAUnbound
3h53A01Unbound UnboundUnboundUnbound
3h53B01Unbound UnboundUnboundUnbound
3h54A01Unbound UnboundBound:A2GUnbound
3h54B01Unbound UnboundBound:A2GUnbound
3h55A01Unbound Analogue:GLA 1500Analogue:GLA 1000Unbound
3h55B01Unbound Analogue:GLA 2500Analogue:GLA 2000Unbound
3iguA01Unbound UnboundUnboundIntermediate-analogue:7JZ
3iguB01Unbound UnboundUnboundIntermediate-analogue:7JZ
1ktbA02Unbound UnboundUnboundUnbound
1ktcA02Unbound UnboundUnboundUnbound
3h53A02Unbound UnboundUnboundUnbound
3h53B02Unbound UnboundUnboundUnbound
3h54A02Unbound UnboundUnboundUnbound
3h54B02Unbound UnboundUnboundUnbound
3h55A02Unbound UnboundUnboundUnbound
3h55B02Unbound UnboundUnboundUnbound
3iguA02Unbound UnboundUnboundUnbound
3iguB02Unbound UnboundUnboundUnbound

Active-site residues
resource
literature [4], [5]
pdbCatalytic residues
         
1ktbA01ASP 61;TYR 103;ASP 140;ARG 197;ASP 201
1ktcA01ASP 61;TYR 103;ASP 140;ARG 197;ASP 201
3h53A01ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3h53B01ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3h54A01ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3h54B01ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3h55A01ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3h55B01ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3iguA01ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3iguB01ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
1ktbA02 
1ktcA02 
3h53A02 
3h53B02 
3h54A02 
3h54B02 
3h55A02 
3h55B02 
3iguA02 
3iguB02 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Figure 4
[5]Fig.6

references
[1]
PubMed ID7712292
JournalCurr Opin Struct Biol
Year1994
Volume4
Pages885-92
AuthorsMcCarter JD, Withers SG
TitleMechanisms of enzymatic glycoside hydrolysis.
[2]
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.
[3]
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.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH N-ACETYLGALACTOSAMINE, GLYCOSYLATION AT ASN-161; ASN-185 AND ASN-369, SUBUNIT, DISULFIDE BONDS.
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.
Related PDB1ktb,1ktc
Related UniProtKBQ90744
[5]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 18-411 IN COMPLEXES WITH N-ACETYLGALACTOSAMINE AND GALACTOSE, DISULFIDE BONDS, GLYCOSYLATION AT ASN-124; ASN-177 AND ASN-385, SUBUNIT, CATALYTIC ACTIVITY, MUTAGENESIS OF ASN-201.
PubMed ID19683538
JournalJ Mol Biol
Year2009
Volume393
Pages435-47
AuthorsClark NE, Garman SC
TitleThe 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases.
Related PDB3h53,3h54,3h55,3igu
Related UniProtKBP17050

comments
This enzyme belongs to glycosidase family-27, with a retaining mechanism.
For this enzyme, both substrate and product are alpha-anomers with an axial configuration at C1 atom, due to the retaining mechanism (see [4]).
According to the literature [4] and [5], the reaction proceeds as follows:
(1) Asp201 acts as a general acid to protonate the leaving N-acetyl-D-galactosaminide. This protonation might form an oxocarbenium-ion like transition-state.
(2) Meanwhile, Asp140 (of 1ktb) makes a nucleophilic attack on the C1 atom of N-acetyl-D-galactosaminide, forming a covalent intermediate with an inverted configuration at C1.
(3) Asp201 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 N-acetyl-D-galactosamine product.
(X) Considering the conservation and relative location of active-site residues, Arg197 modulates the activity of Asp201, whilst Tyr103 modulates the activity of Asp140. Asp61 may stabilize the transition-state through the hydrogen bond with O4 atom.

createdupdated
2010-03-102012-02-01


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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