PDBsum entry: 1odu

Hydrolase

PDB-id: 1odu

Asymmetric unit

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

422 a.a. *

Ligands

FUL ×2

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit, hexamer
- as defined in PDB file (see also PQS)

PDB id:

1odu

Name:

Hydrolase

Title:

Crystal structure of thermotoga maritima alpha-fucosidase in complex with fucose

Structure:

Putative alpha-l-fucosidase. Chain: a, b. Engineered: yes. Other_details: orf tm0306

Source:

Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Biological unit:

Hexamer (from PDB file)

UniProt:

Chains A, B: Q9WYE2 (Q9WYE2_THEMA)

Seq:

Struc:

Seq:

449 a.a.

Struc:

422 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

2.8Å

R-factor:

0.203

R-free:

0.230

Authors:

G.Sulzenbacher,C.Bignon,Y.Bourne,B.Henrissat

Key ref:

G.Sulzenbacher et al. (2004). Crystal structure of Thermotoga maritima alpha-L-fucosidase. Insights into the catalytic mechanism and the molecular basis for fucosidosis.. J Biol Chem, 279, 13119-13128. [PubMed id: 14715651] [DOI: 10.1074/jbc.M313783200]

Date:

14-Mar-03

Release date:

15-Jan-04

Related entries:

1hl8 crystal structure of thermotoga maritima alpha -fucosidase
1hl9 crystal structure of thermotoga maritima alpha -fucosidase in complex with a mechanism based inhibitor

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1074/jbc.M313783200

J Biol Chem 279:13119-13128 (2004)

PubMed id: 14715651

Crystal structure of Thermotoga maritima alpha-L-fucosidase. Insights into the catalytic mechanism and the molecular basis for fucosidosis.

G.Sulzenbacher, C.Bignon, T.Nishimura, C.A.Tarling, S.G.Withers, B.Henrissat, Y.Bourne.

ABSTRACT

Fucosylated glycoconjugates are involved in numerous biological events, and alpha-l-fucosidases, the enzymes responsible for their processing, are therefore of crucial importance. Deficiency in alpha-l-fucosidase activity is associated with fucosidosis, a lysosomal storage disorder characterized by rapid neurodegeneration, resulting in severe mental and motor deterioration. To gain insight into alpha-l-fucosidase function at the molecular level, we have determined the crystal structure of Thermotoga maritima alpha-l-fucosidase. This enzyme assembles as a hexamer and displays a two-domain fold, composed of a catalytic (beta/alpha)(8)-like domain and a C-terminal beta-sandwich domain. The structures of an enzyme-product complex and of a covalent glycosyl-enzyme intermediate, coupled with kinetic and mutagenesis studies, allowed us to identify the catalytic nucleophile, Asp(244), and the Brønsted acid/base, Glu(266). Because T. maritima alpha-l-fucosidase occupies a unique evolutionary position, being far more closely related to the mammalian enzymes than to any other prokaryotic homolog, a structural model of the human enzyme was built to document the structural consequences of the genetic mutations associated with fucosidosis.

Selected figure(s)

Figure 1.
FIG. 1. The catalytic pocket of TM aFuc. Shown are stereo pairs of the 2F[o] - 2F[c] electron density maps for the fucose complex (A) and the fucosyl-enzyme intermediate (B) at 2.8 and 2.25 Å, respectively. Phases were calculated prior to incorporation of the ligand in the refinement, and the maps were contoured at 1.0 . Also shown is a schematic summarizing the interactions between TM aFuc and fucose (C). The ligand is shown in boldface, hydrogen bonds are shown as dashed lines, and van der Waals contacts are shown as pink dotted lines.

Figure 2.
FIG. 2. Overall view of TM aFuc. A, stereo ribbon diagram colored in a gradient along the TM aFuc amino acid sequence, from the N terminus (blue) to the C terminus (red). Secondary structure elements corresponding to the classical ( / )[8]-fold are indicated. The catalytic nucleophile Asp224 and the acid/base Glu266 are shown in ball-and-stick presentation, with carbon atoms colored gray and oxygen atoms colored red. B, the hexameric assembly of TM aFuc, as seen from the top (left) and rotated by 90° (right). For clarity, the trimers composing the hexamer are colored magenta and white, and one trimer is highlighted by a transparent surface representation. Bound fucose molecules are shown in green.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 13119-13128) copyright 2004.

Figures were selected by an automated process.