PDBsum entry 2d44

Hydrolase

PDB id

2d44

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Contents

			Protein chain

					482 a.a. *

			Ligands

					NAG-NAG


					XYS-XYS-AHR ×2

			Waters ×118

* Residue conservation analysis

PDB id:

2d44

Links

Name:

Hydrolase

Title:

Crystal structure of arabinofuranosidase complexed with arabinofuranosyl-alpha-1,2-xylobiose

Structure:

Alpha-l-arabinofuranosidase b. Chain: a. Fragment: residues 19-499. Engineered: yes. Mutation: yes

Source:

Aspergillus kawachii. Organism_taxid: 40384. Expressed in: pichia pastoris. Expression_system_taxid: 4922.

Resolution:

2.30Å

R-factor:

0.203

R-free:

0.250

Authors:

A.Miyanaga,T.Koseki,Y.Miwa,H.Matsuzawa,T.Wakagi,H.Shoun,S.Fushinobu

Key ref:

A.Miyanaga et al. (2006). The family 42 carbohydrate-binding module of family 54 alpha-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose. Biochem J, 399, 503-511. PubMed id: 16846393

Date:

07-Oct-05

Release date:

19-Sep-06

PROCHECK

	Headers

	References

Protein chain

Q8NK89 (ABFB_ASPKW) - Alpha-L-arabinofuranosidase B from Aspergillus kawachii (strain NBRC 4308)

Seq: Struc:					499 a.a. 482 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 2 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.3.2.1.55 - non-reducing end alpha-L-arabinofuranosidase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.

	Biochem J 399:503-511 (2006)
PubMed id: 16846393

The family 42 carbohydrate-binding module of family 54 alpha-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose.
A.Miyanaga, T.Koseki, Y.Miwa, Y.Mese, S.Nakamura, A.Kuno, J.Hirabayashi, H.Matsuzawa, T.Wakagi, H.Shoun, S.Fushinobu.

ABSTRACT

Alpha-L-arabinofuranosidase catalyses the hydrolysis of the alpha-1,2-, alpha-1,3-, and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan. AkAbf54 (the glycoside hydrolase family 54 alpha-L-arabinofuranosidase from Aspergillus kawachii) consists of two domains, a catalytic and an arabinose-binding domain. The latter has been named AkCBM42 [family 42 CBM (carbohydrate-binding module) of AkAbf54] because homologous domains are classified into CBM family 42. In the complex between AkAbf54 and arabinofuranosyl-alpha-1,2-xylobiose, the arabinose moiety occupies the binding pocket of AkCBM42, whereas the xylobiose moiety is exposed to the solvent. AkCBM42 was found to facilitate the hydrolysis of insoluble arabinoxylan, because mutants at the arabinose binding site exhibited markedly decreased activity. The results of binding assays and affinity gel electrophoresis showed that AkCBM42 interacts with arabinose-substituted, but not with unsubstituted, hemicelluloses. Isothermal titration calorimetry and frontal affinity chromatography analyses showed that the association constant of AkCBM42 with the arabinose moiety is approximately 10(3) M(-1). These results indicate that AkCBM42 binds the non-reducing-end arabinofuranosidic moiety of hemicellulose. To our knowledge, this is the first example of a CBM that can specifically recognize the side-chain monosaccharides of branched hemicelluloses.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21212945

B.Seiboth, and B.Metz (2011).
Fungal arabinan and L: -arabinose metabolism.

Appl Microbiol Biotechnol, 89, 1665-1673.

20376631

C.S.Park, M.H.Yoo, K.H.Noh, and D.K.Oh (2010).
Biotransformation of ginsenosides by hydrolyzing the sugar moieties of ginsenosides using microbial glycosidases.

Appl Microbiol Biotechnol, 87, 9.

19908036

D.Guillén, S.Sánchez, and R.Rodríguez-Sanoja (2010).
Carbohydrate-binding domains: multiplicity of biological roles.

Appl Microbiol Biotechnol, 85, 1241-1249.

20333513

O.Guais, O.Tourrasse, M.Dourdoigne, J.L.Parrou, and J.M.Francois (2010).
Characterization of the family GH54 alpha-L-arabinofuranosidases in Penicillium funiculosum, including a novel protein bearing a cellulose-binding domain.

Appl Microbiol Biotechnol, 87, 1007-1021.

19756576

T.Koseki, K.Mochizuki, H.Kisara, A.Miyanaga, S.Fushinobu, T.Murayama, and Y.Shiono (2010).
Characterization of a chimeric enzyme comprising feruloyl esterase and family 42 carbohydrate-binding module.

Appl Microbiol Biotechnol, 86, 155-161.

17955189

B.J.de Wet, M.K.Matthew, K.H.Storbeck, W.H.van Zyl, and B.A.Prior (2008).
Characterization of a family 54 alpha-L: -arabinofuranosidase from Aureobasidium pullulans.

Appl Microbiol Biotechnol, 77, 975-983.

18665359

H.Ichinose, M.Yoshida, Z.Fujimoto, and S.Kaneko (2008).
Characterization of a modular enzyme of exo-1,5-alpha-L: -arabinofuranosidase and arabinan binding module from Streptomyces avermitilis NBRC14893.

Appl Microbiol Biotechnol, 80, 399-408.

18200608

O.Okhrimenko, and I.Jelesarov (2008).
A survey of the year 2006 literature on applications of isothermal titration calorimetry.

J Mol Recognit, 21, 1.

18997327

Z.Fujimoto, H.Ichinose, and S.Kaneko (2008).
Crystallization and preliminary crystallographic analysis of exo-alpha-1,5-L-arabinofuranosidase from Streptomyces avermitilis NBRC14893.

Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 1007-1009.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.