PDBsum entry: 2w46

Hydrolase

PDB id: 2w46

Contents

Protein chains

138 a.a. *

Metals

_NA ×2

_CA ×2

Waters ×423

* Residue conservation analysis

PDB id:

2w46

Name:

Hydrolase

Title:

Cbm35 from cellvibrio japonicus abf62

Structure:

Esterase d. Chain: a, b. Fragment: carbohydrate binding domain, residues 155-298. Synonym: family 35 carbohydrate binding domain. Engineered: yes

Source:

Cellvibrio japonicus. Organism_taxid: 155077. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.90Å R-factor: 0.141 R-free: 0.218

Authors:

C.Montainer,A.Lammerts Van Bueren,C.Dumon,J.E.Flint, M.A.Correia,J.A.Prates,S.Firbank,R.J.Lewis,G.G.Grondin, M.G.Ghinet,T.M.Gloster,C.Herve,J.P.Knox,B.G.Talbot, J.P.Turkenburg,J.Kerovuo,R.Brzezinski,C.M.G.A.Fontes, G.J.Davies,A.B.Boraston ,H.J.Gilbert

Key ref:

C.Montanier et al. (2009). Evidence that family 35 carbohydrate binding modules display conserved specificity but divergent function. Proc Natl Acad Sci U S A, 106, 3065-3070. PubMed id: 19218457 DOI: 10.1073/pnas.0808972106

Date:

21-Nov-08 Release date: 27-Jan-09

Protein chains

Q51815  (Q51815_9GAMM) -  Esterase D

Seq: 583 a.a.

Struc: 138 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: carbohydrate binding (1 term)

DOI no: 10.1073/pnas.0808972106

Proc Natl Acad Sci U S A 106:3065-3070 (2009)

PubMed id: 19218457

Evidence that family 35 carbohydrate binding modules display conserved specificity but divergent function.

C.Montanier, A.L.van Bueren, C.Dumon, J.E.Flint, M.A.Correia, J.A.Prates, S.J.Firbank, R.J.Lewis, G.G.Grondin, M.G.Ghinet, T.M.Gloster, C.Herve, J.P.Knox, B.G.Talbot, J.P.Turkenburg, J.Kerovuo, R.Brzezinski, C.M.Fontes, G.J.Davies, A.B.Boraston, H.J.Gilbert.

ABSTRACT

Enzymes that hydrolyze complex carbohydrates play important roles in numerous biological processes that result in the maintenance of marine and terrestrial life. These enzymes often contain noncatalytic carbohydrate binding modules (CBMs) that have important substrate-targeting functions. In general, there is a tight correlation between the ligands recognized by bacterial CBMs and the substrate specificity of the appended catalytic modules. Through high-resolution structural studies, we demonstrate that the architecture of the ligand binding sites of 4 distinct family 35 CBMs (CBM35s), appended to 3 plant cell wall hydrolases and the exo-beta-D-glucosaminidase CsxA, which contributes to the detoxification and metabolism of an antibacterial fungal polysaccharide, is highly conserved and imparts specificity for glucuronic acid and/or Delta4,5-anhydrogalaturonic acid (Delta4,5-GalA). Delta4,5-GalA is released from pectin by the action of pectate lyases and as such acts as a signature molecule for plant cell wall degradation. Thus, the CBM35s appended to the 3 plant cell wall hydrolases, rather than targeting the substrates of the cognate catalytic modules, direct their appended enzymes to regions of the plant that are being actively degraded. Significantly, the CBM35 component of CsxA anchors the enzyme to the bacterial cell wall via its capacity to bind uronic acid sugars. This latter observation reveals an unusual mechanism for bacterial cell wall enzyme attachment. This report shows that the biological role of CBM35s is not dictated solely by their carbohydrate specificities but also by the context of their target ligands.

Selected figure(s)

Figure 1.
Ligands targeted by the CBM35 domains described in this work. (A) α-1,2 linked GlcA moiety in glucuronoxylan is shown. (B) Δ4,5GalA (4,5anhydrogalactosyl) moiety produced by the action of lyases (β-eliminases) on pectin (a polysaccharide of α-1,4 linked galacturonides) or rhamnogalacturonan is revealed.

Figure 3.
CBM35 structures. (A–D) Ribbon representations, color-ramped from the N-terminus (blue) to C-terminus (red), of Chi-CBM35 (in complex with GlcA) (A), Xyl-CBM35 (in complex with a GlcA containing disaccharide) (B), Rhe-CBM35 (in complex with Δ4,5-GalAα1,4Gal) (C), and Pel-CBM35 (D). The calcium ions are represented as blue spheres and ligands in ball-and-stick representation. Structures are shown in identical orientations. (E–H) Binding sites of Chi-CBM35 in complex with GlcA (E), Chi-CBM35 in complex with Δ4,5-GalAα1,4Gal (F), Xyl-CBM35 in complex with a GlcA containing disaccharide (G), and Rhe-CBM35 in complex with Δ4,5-GalAα1,4Gal (H). (E–H Left) The structures of the active site with the observed electron density for the ligand are shown. The electron density maps are shown as maximum likelihood weighted 2F[obs]-F[calc] maps contoured at 1σ. Stereo views of these maps are given in Fig. S2. (E–H Right) Hydrogen bonding schematics with the calcium atoms are shown as gray circles and water molecules coordinating the calcium are shown as black circles.

Figures were selected by an automated process.