DB code: D00665

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. 3.2.1.49
CSA
M-CSA
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 D00664 D00804 D00863 T00089
2.60.40.1180 : Immunoglobulin-like M00113 T00307 D00165 D00176 D00664 D00863 D00864 M00112 M00193 M00314 T00057 T00062 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam RefSeq
Q90744 Alpha-N-acetylgalactosaminidase
EC 3.2.1.49
Alpha-galactosidase B
GH27 (Glycoside Hydrolase Family 27)
PF02065 (Melibiase)
[Graphical View]
P17050 Alpha-N-acetylgalactosaminidase
EC 3.2.1.49
Alpha-galactosidase B
GH27 (Glycoside Hydrolase Family 27)
PF02065 (Melibiase)
[Graphical View]
NP_000253.1 (Protein)
NM_000262.2 (DNA/RNA sequence)

KEGG enzyme name
Alpha-N-acetylgalactosaminidase
Alpha-acetylgalactosaminidase
N-acetyl-alpha-D-galactosaminidase
N-acetyl-alpha-galactosaminidase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P17050 NAGAB_HUMAN Hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D-galactosaminides. Homodimer. Lysosome.
Q90744 NAGAB_CHICK Hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D-galactosaminides. Homodimer. Lysosome (By similarity).

KEGG Pathways
Map code Pathways E.C.
MAP00603 Glycosphingolipid biosynthesis - globoseries

Compound table
Substrates Products Intermediates
KEGG-id C04134 C00001 C04134 L00046 I00063
E.C.
Compound N-Acetyl-alpha-D-galactosaminide H2O N-Acetyl-alpha-D-galactosaminide N-Acetyl-alpha-D-galactosamine Peptidyl-ASP-beta-N-acetylgalactosaminie
Type amide group,polysaccharide H2O amide group,polysaccharide amide group,carbohydrate
ChEBI 15377
40356
PubChem 22247451
962
84265
1ktbA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1ktcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:NGA Unbound
3h53A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3h53B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3h54A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:A2G Unbound
3h54B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:A2G Unbound
3h55A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:GLA_1500 Analogue:GLA_1000 Unbound
3h55B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:GLA_2500 Analogue:GLA_2000 Unbound
3iguA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Intermediate-analogue:7JZ
3iguB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Intermediate-analogue:7JZ
1ktbA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1ktcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3h53A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3h53B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3h54A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3h54B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3h55A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3h55B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3iguA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
3iguB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [4], [5]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ktbA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 61;TYR 103;ASP 140;ARG 197;ASP 201
1ktcA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 61;TYR 103;ASP 140;ARG 197;ASP 201
3h53A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3h53B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3h54A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3h54B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3h55A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3h55B01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3iguA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
3iguB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 78;TYR 119;ASP 156;ARG 213;ASP 217
1ktbA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1ktcA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3h53A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3h53B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3h54A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3h54B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3h55A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3h55B02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3iguA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3iguB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
Figure 4
[5]
Fig.6

References
[1]
Resource
Comments
Medline ID
PubMed ID 7712292
Journal Curr Opin Struct Biol
Year 1994
Volume 4
Pages 885-92
Authors McCarter JD, Withers SG
Title Mechanisms of enzymatic glycoside hydrolysis.
Related PDB
Related UniProtKB
[2]
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
[3]
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
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH N-ACETYLGALACTOSAMINE, GLYCOSYLATION AT ASN-161; ASN-185 AND ASN-369, SUBUNIT, DISULFIDE BONDS.
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 1ktb 1ktc
Related UniProtKB Q90744
[5]
Resource
Comments X-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.
Medline ID
PubMed ID 19683538
Journal J Mol Biol
Year 2009
Volume 393
Pages 435-47
Authors Clark NE, Garman SC
Title The 1.9 a structure of human alpha-N-acetylgalactosaminidase: The molecular basis of Schindler and Kanzaki diseases.
Related PDB 3h53 3h54 3h55 3igu
Related UniProtKB P17050

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.

Created Updated
2010-03-10 2012-02-01