DB code: D00666

CATH domain 2.60.120.200 : Jelly Rolls Catalytic domain
2.80.10.50 : Trefoil (Acidic Fibroblast Growth Factor, subunit A)
E.C. 3.2.1.55
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
2.80.10.50 : Trefoil (Acidic Fibroblast Growth Factor, subunit A) D00169 M00185
2.60.120.200 : Jelly Rolls S00148 D00535 M00185 S00511 T00064 T00208

Uniprot Enzyme Name
UniprotKB Protein name Synonyms CAZy Pfam
Q8NK89 Alpha-N-arabinofuranosidase B
ABF B
Arabinosidase B
EC 3.2.1.55
CBM42 (Carbohydrate-Binding Module Family 42)
GH54 (Glycoside Hydrolase Family 54)
PF05270 (AbfB)
PF09206 (ArabFuran-catal)
[Graphical View]

KEGG enzyme name
Alpha-N-arabinofuranosidase
Arabinosidase
Alpha-arabinosidase
Alpha-L-arabinosidase
Alpha-arabinofuranosidase
Polysaccharide alpha-L-arabinofuranosidase
Alpha-L-arabinofuranoside hydrolase
L-arabinosidase
Alpha-L-arabinanase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q8NK89 Q8NK89_ASPKA Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides. Secreted (By similarity).

KEGG Pathways
Map code Pathways E.C.
MAP00520 Nucleotide sugars metabolism

Compound table
Substrates Products Intermediates
KEGG-id C01032 C02474 C01889 C00001 C01032 L00047 C02474 C00707 I00109
E.C.
Compound alpha-L-arabinoside alpha-L-Arabinan Arabinoxylan H2O alpha-L-arabinoside alpha-L-arabinofuranose alpha-L-Arabinan Xylan Protein [L-arabinofuranose]-L-Glutamate
Type polysaccharide polysaccharide polysaccharide H2O polysaccharide carbohydrate polysaccharide polysaccharide
ChEBI 15377
28772
PubChem 22247451
962
445935
1wd3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1wd4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Bound:AHR Unbound Unbound
2d43A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2d44A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1wd3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1wd4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2d43A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2d44A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [4], [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1wd3A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 219;GLU 221;ASP 297
1wd4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 219;GLU 221;ASP 297
2d43A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 219;;ASP 297 mutant E221A
2d44A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 219;;ASP 297 mutant E221A
1wd3A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
1wd4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2d43A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
2d44A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
FIG.5
[6]
Fig.6
[7]
Fig.1

References
[1]
Resource
Comments
Medline ID
PubMed ID 9758835
Journal Appl Environ Microbiol
Year 1998
Volume 64
Pages 4021-7
Authors Kaneko S, Arimoto M, Ohba M, Kobayashi H, Ishii T, Kusakabe I
Title Purification and substrate specificities of two alpha-L-arabinofuranosidases from Aspergillus awamori IFO 4033.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 9435077
Journal Appl Environ Microbiol
Year 1998
Volume 64
Pages 216-20
Authors Saha BC, Bothast RJ
Title Purification and characterization of a novel thermostable alpha-L-arabinofuranosidase from a color-variant strain of Aureobasidium pullulans.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 14538102
Journal Biotechnol Adv
Year 2000
Volume 18
Pages 403-23
Authors Saha BC
Title Alpha-L-arabinofuranosidases: biochemistry, molecular biology and application in biotechnology.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 15292273
Journal J Biol Chem
Year 2004
Volume 279
Pages 44907-14
Authors Miyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S
Title Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.
Related PDB 1wd3 1wd4
Related UniProtKB Q9C4B1
[5]
Resource
Comments
Medline ID
PubMed ID 16846393
Journal Biochem J
Year 2006
Volume 399
Pages 503-11
Authors Miyanaga A, Koseki T, Miwa Y, Mese Y, Nakamura S, Kuno A, Hirabayashi J, Matsuzawa H, Wakagi T, Shoun H, Fushinobu S
Title The family 42 carbohydrate-binding module of family 54 alpha-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose.
Related PDB 2d43 2d44
Related UniProtKB Q8NK89
[6]
Resource
Comments
Medline ID
PubMed ID 16385399
Journal J Ind Microbiol Biotechnol
Year 2006
Volume 33
Pages 247-60
Authors Numan MT, Bhosle NB
Title Alpha-L-arabinofuranosidases: the potential applications in biotechnology.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 17002602
Journal Biochem J
Year 2007
Volume 401
Pages 551-8
Authors Wan CF, Chen WH, Chen CT, Chang MD, Lo LC, Li YK
Title Mutagenesis and mechanistic study of a glycoside hydrolase family 54 alpha-L-arabinofuranosidase from Trichoderma koningii.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 17955189
Journal Appl Microbiol Biotechnol
Year 2008
Volume 77
Pages 975-83
Authors de Wet BJ, Matthew MK, Storbeck KH, van Zyl WH, Prior BA
Title Characterization of a family 54 alpha-L-arabinofuranosidase from Aureobasidium pullulans.
Related PDB
Related UniProtKB

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.

Created Updated
2010-03-26 2011-12-07