PDBsum entry: 1wd3

Hydrolase

PDB-id: 1wd3

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PROCHECK

Protein chain

482 a.a. *

Ligands

NAG-NAG

Waters ×362

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1wd3

Name:

Hydrolase

Title:

Crystal structure of arabinofuranosidase

Structure:

Alpha-l-arabinofuranosidase b. Chain: a. Synonym: arabinofuranosidase. Engineered: yes

Source:

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

UniProt:

Q9C4B1 (Q9C4B1_ASPAW)

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:

1.75Å

R-factor:

0.191

R-free:

0.209

Authors:

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

Key ref:

A.Miyanaga et al. (2004). Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.. J Biol Chem, 279, 44907-44914. [PubMed id: 15292273] [DOI: 10.1074/jbc.M405390200]

Date:

11-May-04

Release date:

14-Sep-04

Related entries:

1wd4
the same protein with alpha-l-arabinofuranose

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Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M405390200

J Biol Chem 279:44907-44914 (2004)

PubMed id: 15292273

Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose.

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

ABSTRACT

As the first known structures of a glycoside hydrolase family 54 (GH54) enzyme, we determined the crystal structures of free and arabinose-complex forms of Aspergillus kawachii IFO4308 alpha-l-arabinofuranosidase (AkAbfB). AkAbfB comprises two domains: a catalytic domain and an arabinose-binding domain (ABD). The catalytic domain has a beta-sandwich fold similar to those of clan-B glycoside hydrolases. ABD has a beta-trefoil fold similar to that of carbohydrate-binding module (CBM) family 13. However, ABD shows a number of characteristics distinctive from those of CBM family 13, suggesting that it could be classified into a new CBM family. In the arabinose-complex structure, one of three arabinofuranose molecules is bound to the catalytic domain through many interactions. Interestingly, a disulfide bond formed between two adjacent cysteine residues recognized the arabinofuranose molecule in the active site. From the location of this arabinofuranose and the results of a mutational study, the nucleophile and acid/base residues were determined to be Glu(221) and Asp(297), respectively. The other two arabinofuranose molecules are bound to ABD. The O-1 atoms of the two arabinofuranose molecules bound at ABD are both pointed toward the solvent, indicating that these sites can both accommodate an arabinofuranose side-chain moiety linked to decorated arabinoxylans.

Selected figure(s)

Figure 1.
FIG. 1. Folds of AkAbfB and structurally similar enzymes. Ribbon drawing diagrams of AkAbfB (A), TrSA (B), and -carrageenase (C). Catalytic domains are enclosed in blue dotted lines. The catalytic domain of AkAbfB and structurally similar domains are shown in green. Catalytic residues are shown as ball-and-stick models. A, ABD of AkAbfB is shown in yellow-green. Three arabinofuranose molecules are shown as blue Corey-Pauling-Koltun models. Asn202 and the glycoside chain are shown as Corey-Pauling-Koltun colored ball-and-stick and gray wireframe models, respectively. B, 2-deoxy-2,3-dehydro-N-acetylneuraminic acid molecules are shown as blue Corey-Pauling-Koltun models. D, a topological diagram of the catalytic domain of AkAbfB. The locations of the catalytic residues are indicated by asterisks.

Figure 5.
FIG. 5. The active sites of AkAbfB and GH51 GsAbfA. The O-1 atom of the arabinofuranose molecule in AkAbfB is omitted because its electron density was not observed. A, stereoview of the catalytic center of AkAbfB in a complex with arabinofuranose. Hydrogen bonds and disulfide bond are shown as gray and green dotted lines, respectively. B, stereoview of superimpositioning of AkAbfB in a complex with arabinofuranose and GsAbfA with Ara- (1, 3)-Xyl. AkAbfB and GsAbfA are shown in yellow and cyan, respectively. Only the catalytic residues and important residues for substrate binding are shown. GH51 GsAbfA in a complex with Ara- (1, 3)-Xyl was constructed by combining the structures of the native enzyme (1PZ3 [PDB] ) and Ara- (1, 3)-Xyl complex (1QW8 [PDB] ).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 44907-44914) copyright 2004.

Figures were selected by the author.

Author's comment

ABD of AkAbfB (appeared on Fig. 1A) and homologous sequences have been assigned as Carbohydrate Binding Module family 42 (CBM42) in the CAZy database.
S. Fushinobu.