PDBsum entry 2eab

Hydrolase

PDB id: 2eab

Contents

Protein chains

888 a.a. *

Ligands

EDO ×12

TRS ×4

Metals

_CA ×2

Waters ×3383

* Residue conservation analysis

PDB id:

2eab

Name:

Hydrolase

Title:

Crystal structure of 1,2-a-l-fucosidase from bifidobacterium bifidum (apo form)

Structure:

Alpha-fucosidase. Chain: a, b. Fragment: catalytic domain, residues 0-898. Engineered: yes

Source:

Bifidobacterium bifidum. Organism_taxid: 1681. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.12Å R-factor: 0.176 R-free: 0.189

Authors:

M.Nagae,A.Tsuchiya,T.Katayama,K.Yamamoto,S.Wakatsuki,R.Kato

Key ref:

M.Nagae et al. (2007). Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum. J Biol Chem, 282, 18497-18509. PubMed id: 17459873 DOI: 10.1074/jbc.M702246200

Date:

31-Jan-07 Release date: 24-Apr-07

Protein chains

Q6JV24  (Q6JV24_BIFBI) -  Alpha-fucosidase from Bifidobacterium bifidum

Seq: 1959 a.a.

Struc: 888 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.63 - 1,2-alpha-L-fucosidase.
• Reaction: methyl-2-alpha-L-fucopyranosyl-beta-D-galactoside + H2O = methyl beta-D- galactoside + L-fucose

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M702246200

J Biol Chem 282:18497-18509 (2007)

PubMed id: 17459873

Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum.

M.Nagae, A.Tsuchiya, T.Katayamka, K.Yamamoto, S.Wakatsuki, R.Kato.

ABSTRACT

1,2-alpha-L-Fucosidase (AfcA), which hydrolyzes the glycosidic linkage of Fucalpha1-2Gal via an inverting mechanism, was recently isolated from Bifidobacterium bifidum and classified as the first member of the novel glycoside hydrolase family 95 (GH95). To better understand the molecular mechanism of this enzyme, we determined the X-ray crystal structures of the AfcA catalytic (Fuc) domain in unliganded and complexed forms with deoxyfuconojirimycin (inhibitor), 2'-fucosyllactose (substrate), and L-fucose and lactose (products) at 1.12-2.10 A resolution. The AfcA Fuc domain is composed of four regions, an N-terminal beta region, a helical linker, an (alpha/alpha)6 helical barrel domain, and a C-terminal beta region, and this arrangement is similar to bacterial phosphorylases. In the complex structures, the ligands were buried in the central cavity of the helical barrel domain. Structural analyses in combination with mutational experiments revealed that the highly conserved Glu566 likely acts as a general acid catalyst. However, no carboxylic acid residue is found at the appropriate position for a general base catalyst. Instead, a water molecule stabilized by Asn423 in the substrate-bound complex is suitably located to perform a nucleophilic attack on the C1 atom of L-fucose moiety in 2'-fucosyllactose, and its location is nearly identical near the O1 atom of beta-L-fucose in the products-bound complex. Based on these data, we propose and discuss a novel catalytic reaction mechanism of AfcA.

Selected figure(s)

Figure 1.
FIGURE 1. Crystal structure of B. bifidum AfcA fucosidase catalytic domain (Fuc domain). a, ribbon model of the Fuc domain is shown. The N-terminal region, helical linker region, central helical barrel domain, and C-terminal region are colored in blue, cyan, yellow, and red, respectively. b, electrostatic surface potential map of the Fuc domain. Positive (blue) and negative (red) potentials are mapped on the van der Waals surfaces in the range -10 K[b]T (red) to +10 K[b]T (blue), where K[b] is Boltzmann's constant and T is the absolute temperature.

Figure 6.
FIGURE 6. Proposed catalytic reaction mechanism of the AfcA fucosidase. Hydrogen bonds are depicted by dotted lines. The directions of nucleophilic attack and proton donation are indicated by blank arrows.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 18497-18509) copyright 2007.

Figures were selected by the author.