PDBsum entry 3d30

Peptidoglycan-binding protein

PDB id: 3d30

Contents

Protein chain

208 a.a. *

Ligands

GOL

FMT ×3

Waters ×230

* Residue conservation analysis

PDB id:

3d30

Name:

Peptidoglycan-binding protein

Title:

Structure of an expansin like protein from bacillus subtilis at 1.9a resolution

Structure:

Expansin like protein. Chain: a. Synonym: yoaj. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Strain: 168. Gene: yoaj, bsu18630. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.165 R-free: 0.191

Authors:

F.Kerff,S.Petrella,R.Herman,E.Sauvage,B.Joris,P.Charlier

Key ref:

F.Kerff et al. (2008). Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization. Proc Natl Acad Sci U S A, 105, 16876-16881. PubMed id: 18971341 DOI: 10.1073/pnas.0809382105

Date:

09-May-08 Release date: 14-Oct-08

Protein chain

O34918  (YOAJ_BACSU) -  Expansin-YoaJ from Bacillus subtilis (strain 168)

Seq: 232 a.a.

Struc: 208 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1073/pnas.0809382105

Proc Natl Acad Sci U S A 105:16876-16881 (2008)

PubMed id: 18971341

Crystal structure and activity of Bacillus subtilis YoaJ (EXLX1), a bacterial expansin that promotes root colonization.

F.Kerff, A.Amoroso, R.Herman, E.Sauvage, S.Petrella, P.Filée, P.Charlier, B.Joris, A.Tabuchi, N.Nikolaidis, D.J.Cosgrove.

ABSTRACT

We solved the crystal structure of a secreted protein, EXLX1, encoded by the yoaJ gene of Bacillus subtilis. Its structure is remarkably similar to that of plant beta-expansins (group 1 grass pollen allergens), consisting of 2 tightly packed domains (D1, D2) with a potential polysaccharide-binding surface spanning the 2 domains. Domain D1 has a double-psi beta-barrel fold with partial conservation of the catalytic site found in family 45 glycosyl hydrolases and in the MltA family of lytic transglycosylases. Domain D2 has an Ig-like fold similar to group 2/3 grass pollen allergens, with structural features similar to a type A carbohydrate-binding domain. EXLX1 bound to plant cell walls, cellulose, and peptidoglycan, but it lacked lytic activity against a variety of plant cell wall polysaccharides and peptidoglycan. EXLX1 promoted plant cell wall extension similar to, but 10 times weaker than, plant beta-expansins, which synergistically enhanced EXLX1 activity. Deletion of the gene encoding EXLX1 did not affect growth or peptidoglycan composition of B. subtilis in liquid medium, but slowed lysis upon osmotic shock and greatly reduced the ability of the bacterium to colonize maize roots. The presence of EXLX1 homologs in a small but diverse set of plant pathogens further supports a role in plant-bacterial interactions. Because plant expansins have proved difficult to express in active form in heterologous systems, the discovery of a bacterial homolog opens the door for detailed structural studies of expansin function.

Selected figure(s)

Figure 1.
Structure of EXLX1 and comparison with other proteins containing a double-ψ β-barrel fold and interacting with polysaccharides. (A) Diagram representation of EXLX1: D1, cyan; D2, magenta. (B) Diagram representations of EXLX1 and EXPB1 (orange) superimposed. (C) Diagram representations of EXLX1 and EcMltA(D308A)–chitohexaose superimposed. The chitohexaose [(GlcNAc)[6]] is shown as sticks. Nt, N-terminal extension. (D) Diagram representations of GH45 endoglucanase MeCel45A and EXPB1 superimposed. (E) Diagram and surface representation of EXLX1 with chitohexaose (in sticks) from the superimposed EcMltA(D308A)–chitohexahose. The most conserved residues in proteins with a double-ψ β-barrel fold are highlighted in yellow. EXLX1 is oriented with shallow groove on the front instead of on top as in A–D.

Figure 3.
Cell wall loosening activity of EXLX1. Two representative examples are shown of EXLX1-induced extension in heat-inactivated wheat coleoptile walls. (Inset) Dependence of induced extension rate (micrometers per minute) on applied EXLX1 concentration (micrograms per milliliter). The points are means ± SEM of 8–12 replicates.

Figures were selected by an automated process.