DB code: M00314

RLCP classification 1.30.46030.482 : Hydrolysis
CATH domain 3.20.110.10 : 7-stranded beta/alpha barrel Catalytic domain
1.-.-.- : Catalytic domain
2.60.40.1180 : Immunoglobulin-like
2.70.98.30 : Beta-galactosidase; Chain A, domain 5
2.60.40.1360 : Immunoglobulin-like
E.C. 3.2.1.24
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
2.60.40.1180 : Immunoglobulin-like M00113 T00307 D00165 D00176 D00664 D00665 D00863 D00864 M00112 M00193 T00057 T00062 T00067

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Contains RefSeq CAZy Pfam
Q99YP5
Alpha-mannosidase
EC 3.2.1.24
None NP_269660.1 (Protein)
NC_002737.1 (DNA/RNA sequence)
YP_282680.1 (Protein)
NC_007297.1 (DNA/RNA sequence)
GH38 (Glycoside Hydrolase Family 38)
PF09261 (Alpha-mann_mid)
PF01074 (Glyco_hydro_38)
PF07748 (Glyco_hydro_38C)
[Graphical View]
Q29451 Lysosomal alpha-mannosidase
Laman
EC 3.2.1.24
Lysosomal acid alpha-mannosidase
Mannosidase alpha class 2B member 1
Mannosidase alpha-B
Lysosomal alpha-mannosidase A peptide
Lysosomal alpha-mannosidase B peptide
Lysosomal alpha-mannosidase C peptide
Lysosomal alpha-mannosidase D peptide
Lysosomal alpha-mannosidase E peptide
NP_776986.2 (Protein)
NM_174561.2 (DNA/RNA sequence)
GH38 (Glycoside Hydrolase Family 38)
PF09261 (Alpha-mann_mid)
PF01074 (Glyco_hydro_38)
PF07748 (Glyco_hydro_38C)
[Graphical View]

KEGG enzyme name
Alpha-mannosidase
Alpha-D-mannosidase
p-Nitrophenyl-alpha-mannosidase
Alpha-D-mannopyranosidase
1,2-Alpha-mannosidase
1,2-Alpha-D-mannosidase
Exo-alpha-mannosidase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q29451 MA2B1_BOVIN Hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides. Homodimer. Lysosome. Binds 1 zinc ion per subunit.
Q99YP5 Q99YP5_STRP1

KEGG Pathways
Map code Pathways E.C.
MAP00511 N-Glycan degradation

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C02603 C00001 C02603 C00936
E.C.
Compound Zinc alpha-D-Mannoside H2O alpha-D-Mannoside alpha-D-Mannose
Type heavy metal carbohydrate H2O carbohydrate carbohydrate
ChEBI 29105
15377
28729
PubChem 32051
22247451
962
185698
2wyhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_Zn Unbound Unbound Unbound
2wyhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_Zn Unbound Unbound Unbound
2wyiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_Zn Unbound Unbound Analogue:SWA
2wyiB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_Zn Unbound Unbound Analogue:SWA
1o7dA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_Zn Unbound Unbound Unbound
1o7dB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyiB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1o7dC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyhA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyhB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyiA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyiB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1o7dC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyhA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyhB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyiA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyiB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1o7dD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyhA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyhB05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyiA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
2wyiB05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1o7dE 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 [3], [4] & Swiss-prot;Q29451

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
2wyhA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 125;ARG 149;TYR 192;ASP 232 HIS 13;ASP 15;ASP 125(Zinc binding)
2wyhB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 125;ARG 149;TYR 192;ASP 232 HIS 13;ASP 15;ASP 125(Zinc binding)
2wyiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 125;ARG 149;TYR 192;ASP 232 HIS 13;ASP 15;ASP 125(Zinc binding)
2wyiB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 125;ARG 149;TYR 192;ASP 232 HIS 13;ASP 15;ASP 125(Zinc binding)
1o7dA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 196;ARG 220;TYR 261;ASP 319 HIS 72;ASP 74;ASP 196(Zinc binding)
1o7dB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyhA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 351(Zinc binding)
2wyhB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 351(Zinc binding)
2wyiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 351(Zinc binding)
2wyiB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 351(Zinc binding)
1o7dC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 446(Zinc binding)
2wyhA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyhB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyiA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyiB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1o7dC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyhA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyhB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyiA04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyiB04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1o7dD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyhA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyhB05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyiA05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2wyiB05 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1o7dE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.635, p.637
[4]
Fig.5

References
[1]
Resource
Comments
Medline ID
PubMed ID 9325188
Journal Biochem Biophys Res Commun
Year 1997
Volume 238
Pages 896-8
Authors Howard S, Braun C, McCarter J, Moremen KW, Liao YF, Withers SG
Title Human lysosomal and jack bean alpha-mannosidases are retaining glycosidases.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 11078873
Journal FEBS Lett
Year 2000
Volume 484
Pages 175-8
Authors Numao S, He S, Evjen G, Howard S, Tollersrud OK, Withers SG
Title Identification of Asp197 as the catalytic nucleophile in the family 38 alpha-mannosidase from bovine kidney lysosomes.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 52-999.
Medline ID
PubMed ID 12634058
Journal J Mol Biol
Year 2003
Volume 327
Pages 631-44
Authors Heikinheimo P, Helland R, Leiros HK, Leiros I, Karlsen S, Evjen G, Ravelli R, Schoehn G, Ruigrok R, Tollersrud OK, McSweeney S, Hough E
Title The structure of bovine lysosomal alpha-mannosidase suggests a novel mechanism for low-pH activation.
Related PDB 1o7d
Related UniProtKB Q29451
[4]
Resource
Comments
Medline ID
PubMed ID 20140249
Journal PLoS One
Year 2010
Volume 5
Pages e9006
Authors Suits MD, Zhu Y, Taylor EJ, Walton J, Zechel DL, Gilbert HJ, Davies GJ
Title Structure and kinetic investigation of Streptococcus pyogenes family GH38 alpha-mannosidase.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to glycosyl hydrolase family-38.
Although the nucleophilic residue, Asp125 (of 2wyh), is bound to zinc ion in the apo enzyme, it does not seem to be bound to the zinc ion while the substrate/product is bound to the active site on this enzyme. During the reaction, the zinc ion is bound to the hydroxyl groups of the mannoside, as well as to His13 and Asp15. Thus, the reaction of this enzyme proceeds as follows (see [3] & [4]):
(0) Arg149 and Tyr192 modulate the activity of the nucleophilic residue, Asp125, by interacting with it.
(1) Asp232 acts as a general acid to protonate the oxygen atom of the leaving group, leading to the formation of oxocarbenium-ion like transition-state (in a 1S5 skew-boat conformation). Here, the skew-boat conformation of the transition-state seems to be stabilized by the zinc ion, which is bound to His13 and Asp15.
(2) Asp125 makes a nucleophilic attack on the C1 atom of the alpha-mannoside in the oxocarbenium-ion like transition-state, forming a covalent glycosyl-enzyme intermediate. (This nucleophilic substitution seems to be SN1-like raction.)
(3) Asp232 now acts as a general base to activate a water molecule. The activated water makes a nucleophilic attack on the glycosyl-enzyme intermediate, leading to the formation of oxocarbenium-ion like transition-state. The transition-state is also stabilized by the zinc ion.
(4) Finally, the bond between the alpha-mannose and Asp125 is cleaved, while the bond between the alpha-mannose and the activated water is formed, to complete the reaction.

Created Updated
2010-08-02 2011-05-26