PDBsum entry: 2d43

Hydrolase

PDB-id: 2d43

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Protein chain

482 a.a. *

Ligands

NAG-NAG

AHR-AHR ×2

Waters ×59

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2d43

Name:

Hydrolase

Title:

Crystal structure of arabinofuranosidase complexed with arabinotriose

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.

UniProt:

Q8NK89 (Q8NK89_ASPKA)

Seq:

Struc:

Seq:

499 a.a.

Struc:

482 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

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

Enzyme class:

E.C.3.2.1.55   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

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

Resolution:

2.80Å

R-factor:

0.199

R-free:

0.248

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] [DOI: 10.1042/BJ20060567]

Date:

07-Oct-05

Release date:

19-Sep-06

Related entries:

1wd3
1wd4
2d44
the same protein complexed with arabinofuranosyl-alpha-1,2-
xylobiose

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Key reference

DOI no: 10.1042/BJ20060567

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.