EzCatDB: D00666
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DB codeD00666
CATH domainDomain 12.60.120.200 : Jelly RollsCatalytic domain
Domain 22.80.10.50 : Trefoil (Acidic Fibroblast Growth Factor, subunit A)
E.C.3.2.1.55

CATH domainRelated DB codes (homologues)
2.60.120.200 : Jelly RollsS00148,D00535,M00185,S00511,T00064,T00208
2.80.10.50 : Trefoil (Acidic Fibroblast Growth Factor, subunit A)D00169,M00185

Enzyme Name
UniProtKBKEGG

Q8NK89
Protein nameAlpha-N-arabinofuranosidase BAlpha-N-arabinofuranosidase
Arabinosidase
Alpha-arabinosidase
Alpha-L-arabinosidase
Alpha-arabinofuranosidase
Polysaccharide alpha-L-arabinofuranosidase
Alpha-L-arabinofuranoside hydrolase
L-arabinosidase
Alpha-L-arabinanase
SynonymsABF B
Arabinosidase B
EC 3.2.1.55
PfamPF05270 (AbfB)
PF09206 (ArabFuran-catal)
[Graphical view]
CAZyGH54 (Glycoside Hydrolase Family)

KEGG pathways
MAP codePathways
MAP00520Nucleotide sugars metabolism

UniProtKB:Accession NumberQ8NK89
Entry nameQ8NK89_ASPKA
ActivityHydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.
Subunit
Subcellular locationSecreted (By similarity).
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProductsintermediates
KEGG-idC01032C02474C01889C00001C01032L00047C02474C00707I00109
Compoundalpha-L-arabinosidealpha-L-ArabinanArabinoxylanH2Oalpha-L-arabinosidealpha-L-arabinofuranosealpha-L-ArabinanXylanProtein [L-arabinofuranose]-L-Glutamate
TypepolysaccharidepolysaccharidepolysaccharideH2Opolysaccharidecarbohydratepolysaccharidepolysaccharide
ChEBI


15377

28772



PubChem


962
22247451

445935



                 
1wd3A01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1wd4A01UnboundUnboundUnbound UnboundBound:AHRUnboundUnbound 
2d43A01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2d44A01UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1wd3A02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
1wd4A02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2d43A02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 
2d44A02UnboundUnboundUnbound UnboundUnboundUnboundUnbound 

Active-site residues
resource
literature [4], [7]
pdbCatalytic residuescomment
          
1wd3A01ASP 219;GLU 221;ASP 297
 
1wd4A01ASP 219;GLU 221;ASP 297
 
2d43A01ASP 219;       ;ASP 297
mutant E221A
2d44A01ASP 219;       ;ASP 297
mutant E221A
1wd3A02 
 
1wd4A02 
 
2d43A02 
 
2d44A02 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]FIG.5
[6]Fig.6
[7]Fig.1

references
[1]
PubMed ID9758835
JournalAppl Environ Microbiol
Year1998
Volume64
Pages4021-7
AuthorsKaneko S, Arimoto M, Ohba M, Kobayashi H, Ishii T, Kusakabe I
TitlePurification and substrate specificities of two alpha-L-arabinofuranosidases from Aspergillus awamori IFO 4033.
[2]
PubMed ID9435077
JournalAppl Environ Microbiol
Year1998
Volume64
Pages216-20
AuthorsSaha BC, Bothast RJ
TitlePurification and characterization of a novel thermostable alpha-L-arabinofuranosidase from a color-variant strain of Aureobasidium pullulans.
[3]
PubMed ID14538102
JournalBiotechnol Adv
Year2000
Volume18
Pages403-23
AuthorsSaha BC
TitleAlpha-L-arabinofuranosidases: biochemistry, molecular biology and application in biotechnology.
[4]
PubMed ID15292273
JournalJ Biol Chem
Year2004
Volume279
Pages44907-14
AuthorsMiyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S
TitleCrystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.
Related PDB1wd3,1wd4
Related UniProtKBQ9C4B1
[5]
PubMed ID16846393
JournalBiochem J
Year2006
Volume399
Pages503-11
AuthorsMiyanaga A, Koseki T, Miwa Y, Mese Y, Nakamura S, Kuno A, Hirabayashi J, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S
TitleThe family 42 carbohydrate-binding module of family 54 alpha-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose.
Related PDB2d43,2d44
Related UniProtKBQ8NK89
[6]
PubMed ID16385399
JournalJ Ind Microbiol Biotechnol
Year2006
Volume33
Pages247-60
AuthorsNuman MT, Bhosle NB
TitleAlpha-L-arabinofuranosidases: the potential applications in biotechnology.
[7]
PubMed ID17002602
JournalBiochem J
Year2007
Volume401
Pages551-8
AuthorsWan CF, Chen WH, Chen CT, Chang MD, Lo LC, Li YK
TitleMutagenesis and mechanistic study of a glycoside hydrolase family 54 alpha-L-arabinofuranosidase from Trichoderma koningii.
[8]
PubMed ID17955189
JournalAppl Microbiol Biotechnol
Year2008
Volume77
Pages975-83
Authorsde Wet BJ, Matthew MK, Storbeck KH, van Zyl WH, Prior BA
TitleCharacterization of a family 54 alpha-L-arabinofuranosidase from Aureobasidium pullulans.

comments
According to the literature [4], Alpha-N-arabinofuranosidases belong to five glycosidase families,3, 43, 51, 54, and 62. Glycosidase family-3, family-51, and family-54 are retaining enzymes, whereas family-43 is an inverting enzyme family (see [4]). Family-3 and family-51 adopt (alpha/beta)8 barrel fold (CATH 3.20.20.-), whereaas family-43 and family-62 seem to adopt beta-propeller fold (CATH 2.115.10.20).
This enzyme belongs to the glycosidase family-54, with a retaining mechanism.
According to the literature [7], Asp219 is involved in catalysis. However, its catalytic role has not been elucidated yet.
According to the literature [4], [6] and [7], the catalytic reaction proceeds as follows:
(1) Asp297 acts as a general acid to protonate the leaving O3 atom of Xylose group, whereas Glu221 makes a nucleophilic attack on C1 atom of L-arabinose group, forming a covalent arabinosyl-enzyme intermediate.
(2) Asp297 acts as a general base to activate a water molecule.
(3) The activated water molecule makes a nucleophilic attack on C1 atom, leading to the deglycosylation of Glu221.

createdupdated
2010-03-262011-12-07


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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