EzCatDB: M00314
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DB codeM00314
RLCP classification1.30.46030.482 : Hydrolysis
CATH domainDomain 13.20.110.10 : 7-stranded beta/alpha barrelCatalytic domain
Domain 21.-.-.-Catalytic domain
Domain 32.60.40.1180 : Immunoglobulin-like
Domain 42.70.98.30 : Beta-galactosidase; Chain A, domain 5
Domain 52.60.40.1360 : Immunoglobulin-like
E.C.3.2.1.24

CATH domainRelated DB codes (homologues)
2.60.40.1180 : Immunoglobulin-likeM00113,T00307,D00165,D00176,D00664,D00665,D00863,D00864,M00112,M00193,T00057,T00062,T00067

Enzyme Name
UniProtKBKEGG

Q99YP5Q29451
Protein name
Lysosomal alpha-mannosidaseAlpha-mannosidase
Alpha-D-mannosidase
p-Nitrophenyl-alpha-mannosidase
Alpha-D-mannopyranosidase
1,2-Alpha-mannosidase
1,2-Alpha-D-mannosidase
Exo-alpha-mannosidase
SynonymsAlpha-mannosidase
EC 3.2.1.24
Laman
EC 3.2.1.24
Lysosomal acid alpha-mannosidase
Mannosidase alpha class 2B member 1
Mannosidase alpha-B
ContainsNoneLysosomal alpha-mannosidase A peptide
Lysosomal alpha-mannosidase B peptide
Lysosomal alpha-mannosidase C peptide
Lysosomal alpha-mannosidase D peptide
Lysosomal alpha-mannosidase E peptide
RefSeqNP_269660.1 (Protein)
NC_002737.1 (DNA/RNA sequence)
YP_282680.1 (Protein)
NC_007297.1 (DNA/RNA sequence)
NP_776986.2 (Protein)
NM_174561.2 (DNA/RNA sequence)
PfamPF09261 (Alpha-mann_mid)
PF01074 (Glyco_hydro_38)
PF07748 (Glyco_hydro_38C)
[Graphical view]
PF09261 (Alpha-mann_mid)
PF01074 (Glyco_hydro_38)
PF07748 (Glyco_hydro_38C)
[Graphical view]
CAZyGH38 (Glycoside Hydrolase Family)
GH38 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00511N-Glycan degradation

UniProtKB:Accession NumberQ99YP5Q29451
Entry nameQ99YP5_STRP1MA2B1_BOVIN
Activity
Hydrolysis of terminal, non-reducing alpha-D-mannose residues in alpha-D-mannosides.
Subunit
Homodimer.
Subcellular location
Lysosome.
Cofactor
Binds 1 zinc ion per subunit.

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00038C02603C00001C02603C00936
CompoundZincalpha-D-MannosideH2Oalpha-D-Mannosidealpha-D-Mannose
Typeheavy metalcarbohydrateH2Ocarbohydratecarbohydrate
ChEBI29105

15377

28729
PubChem32051

962
22247451

185698
             
2wyhA01Bound:_ZnUnbound UnboundUnbound
2wyhB01Bound:_ZnUnbound UnboundUnbound
2wyiA01Bound:_ZnUnbound UnboundAnalogue:SWA
2wyiB01Bound:_ZnUnbound UnboundAnalogue:SWA
1o7dABound:_ZnUnbound UnboundUnbound
1o7dBUnboundUnbound UnboundUnbound
2wyhA02UnboundUnbound UnboundUnbound
2wyhB02UnboundUnbound UnboundUnbound
2wyiA02UnboundUnbound UnboundUnbound
2wyiB02UnboundUnbound UnboundUnbound
1o7dC01UnboundUnbound UnboundUnbound
2wyhA03UnboundUnbound UnboundUnbound
2wyhB03UnboundUnbound UnboundUnbound
2wyiA03UnboundUnbound UnboundUnbound
2wyiB03UnboundUnbound UnboundUnbound
1o7dC02UnboundUnbound UnboundUnbound
2wyhA04UnboundUnbound UnboundUnbound
2wyhB04UnboundUnbound UnboundUnbound
2wyiA04UnboundUnbound UnboundUnbound
2wyiB04UnboundUnbound UnboundUnbound
1o7dDUnboundUnbound UnboundUnbound
2wyhA05UnboundUnbound UnboundUnbound
2wyhB05UnboundUnbound UnboundUnbound
2wyiA05UnboundUnbound UnboundUnbound
2wyiB05UnboundUnbound UnboundUnbound
1o7dEUnboundUnbound UnboundUnbound

Active-site residues
resource
Literature [3], [4] & Swiss-prot;Q29451
pdbCatalytic residuesCofactor-binding residues
          
2wyhA01ASP 125;ARG 149;TYR 192;ASP 232
HIS 13;ASP 15;ASP 125(Zinc binding)
2wyhB01ASP 125;ARG 149;TYR 192;ASP 232
HIS 13;ASP 15;ASP 125(Zinc binding)
2wyiA01ASP 125;ARG 149;TYR 192;ASP 232
HIS 13;ASP 15;ASP 125(Zinc binding)
2wyiB01ASP 125;ARG 149;TYR 192;ASP 232
HIS 13;ASP 15;ASP 125(Zinc binding)
1o7dAASP 196;ARG 220;TYR 261;ASP 319
HIS 72;ASP 74;ASP 196(Zinc binding)
1o7dB 
 
2wyhA02 
HIS 351(Zinc binding)
2wyhB02 
HIS 351(Zinc binding)
2wyiA02 
HIS 351(Zinc binding)
2wyiB02 
HIS 351(Zinc binding)
1o7dC01 
HIS 446(Zinc binding)
2wyhA03 
 
2wyhB03 
 
2wyiA03 
 
2wyiB03 
 
1o7dC02 
 
2wyhA04 
 
2wyhB04 
 
2wyiA04 
 
2wyiB04 
 
1o7dD 
 
2wyhA05 
 
2wyhB05 
 
2wyiA05 
 
2wyiB05 
 
1o7dE 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.635, p.637
[4]Fig.5

references
[1]
PubMed ID9325188
JournalBiochem Biophys Res Commun
Year1997
Volume238
Pages896-8
AuthorsHoward S, Braun C, McCarter J, Moremen KW, Liao YF, Withers SG
TitleHuman lysosomal and jack bean alpha-mannosidases are retaining glycosidases.
[2]
PubMed ID11078873
JournalFEBS Lett
Year2000
Volume484
Pages175-8
AuthorsNumao S, He S, Evjen G, Howard S, Tollersrud OK, Withers SG
TitleIdentification of Asp197 as the catalytic nucleophile in the family 38 alpha-mannosidase from bovine kidney lysosomes.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 52-999.
PubMed ID12634058
JournalJ Mol Biol
Year2003
Volume327
Pages631-44
AuthorsHeikinheimo P, Helland R, Leiros HK, Leiros I, Karlsen S, Evjen G, Ravelli R, Schoehn G, Ruigrok R, Tollersrud OK, McSweeney S, Hough E
TitleThe structure of bovine lysosomal alpha-mannosidase suggests a novel mechanism for low-pH activation.
Related PDB1o7d
Related UniProtKBQ29451
[4]
PubMed ID20140249
JournalPLoS One
Year2010
Volume5
Pagese9006
AuthorsSuits MD, Zhu Y, Taylor EJ, Walton J, Zechel DL, Gilbert HJ, Davies GJ
TitleStructure and kinetic investigation of Streptococcus pyogenes family GH38 alpha-mannosidase.

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.

createdupdated
2010-08-022011-05-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
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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)
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