PDBsum entry: 2vpt

Hydrolase

PDB id: 2vpt

Contents

Protein chain

201 a.a. *

Metals

_CA

Waters ×247

* Residue conservation analysis

PDB id:

2vpt

Name:

Hydrolase

Title:

Clostridium thermocellum family 3 carbohydrate esterase

Structure:

Lipolytic enzyme. Chain: a. Fragment: catalytic domain, residues 32-237. Synonym: family 3 carbohydrate esterase. Engineered: yes

Source:

Clostridium thermocellum. Organism_taxid: 1515. Atcc: 27405. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.40Å R-factor: 0.154 R-free: 0.175

Authors:

M.A.S.Correia,J.A.M.Prates,J.Bras,C.M.G.A.Fontes,J.A.Newman, R.J.Lewis,H.J.Gilbert,J.E.Flint

Key ref:

M.A.Correia et al. (2008). Crystal structure of a cellulosomal family 3 carbohydrate esterase from Clostridium thermocellum provides insights into the mechanism of substrate recognition. J Mol Biol, 379, 64-72. PubMed id: 18436237 DOI: 10.1016/j.jmb.2008.03.037

Date:

04-Mar-08 Release date: 06-May-08

Protein chain

A3DDK4  (A3DDK4_CLOTH) -  Lipolytic protein G-D-S-L family

Seq: 528 a.a.

Struc: 201 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: lipid metabolic process (1 term)
• Biochemical function: hydrolase activity (2 terms)

DOI no: 10.1016/j.jmb.2008.03.037

J Mol Biol 379:64-72 (2008)

PubMed id: 18436237

Crystal structure of a cellulosomal family 3 carbohydrate esterase from Clostridium thermocellum provides insights into the mechanism of substrate recognition.

M.A.Correia, J.A.Prates, J.Brás, C.M.Fontes, J.A.Newman, R.J.Lewis, H.J.Gilbert, J.E.Flint.

ABSTRACT

The microbial degradation of the plant cell wall is of increasing industrial significance, exemplified by the interest in generating biofuels from plant cell walls. The majority of plant cell-wall polysaccharides are acetylated, and removal of the acetyl groups through the action of carbohydrate esterases greatly increases the efficiency of polysaccharide saccharification. Enzymes in carbohydrate esterase family 3 (CE3) are common in plant cell wall-degrading microorganisms but there is a paucity of structural and biochemical information on these biocatalysts. Clostridium thermocellum contains a single CE3 enzyme, CtCes3, which comprises two highly homologous (97% sequence identity) catalytic modules appended to a C-terminal type I dockerin that targets the esterase into the cellulosome, a large protein complex that catalyses plant cell wall degradation. Here, we report the crystal structure and biochemical properties of the N-terminal catalytic module (CtCes3-1) of CtCes3. The enzyme is a thermostable acetyl-specific esterase that exhibits a strong preference for acetylated xylan. CtCes3-1 displays an alpha/beta hydrolase fold that contains a central five-stranded parallel twisted beta-sheet flanked by six alpha-helices. In addition, the enzyme contains a canonical catalytic triad in which Ser44 is the nucleophile, His208 is the acid-base and Asp205 modulates the basic nature of the histidine. The acetate moiety is accommodated in a hydrophobic pocket and the negative charge of the tetrahedral transition state is stabilized through hydrogen bonds with the backbone N of Ser44 and Gly95 and the side-chain amide of Asn124.

Selected figure(s)

Figure 1.
Fig. 1. Structure of the CtCes3-1 monomer coloured as a blue to red gradient from the N terminus to the C terminus with key secondary structural elements labelled. This and all subsequent molecular graphics images were prepared using the program PYMOL [http://pymol.sourceforge.net/].

Figure 2.
Fig. 2. The 1.4 Å resolution 2F[o]–1F[c] electron density map contoured at 2σ covering the final refined coordinates of CtCes3-1 in the vicinity of the calcium ion-binding site. Residues are shown in stick format and coloured according to atom type with carbon yellow, the calcium ion (shown as a green sphere) is coordinated by the side chain of three Asp residues, the main-chain carbonyl of Phe44 and two water molecules (shown as red spheres) in a pentagonal bipyramidal geometry.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 379, 64-72) copyright 2008.

Figures were selected by an automated process.