DB code: D00666

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

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 15377		28772 28772
PubChem				22247451 962 22247451 962		445935 445935

1wd3A01	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound
1wd4A01	Unbound	Unbound	Unbound		Unbound	Bound:AHR	Unbound	Unbound
2d43A01	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound
2d44A01	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound
1wd3A02	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound
1wd4A02	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound
2d43A02	Unbound	Unbound	Unbound		Unbound	Unbound	Unbound	Unbound
2d44A02	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	ASP 219;GLU 221;ASP 297
1wd4A01	ASP 219;GLU 221;ASP 297
2d43A01	ASP 219;;ASP 297				mutant E221A
2d44A01	ASP 219;;ASP 297				mutant E221A
1wd3A02
1wd4A02
2d43A02
2d44A02

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.

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