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PDBsum entry 3d30
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Peptidoglycan-binding protein
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PDB id
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3d30
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References listed in PDB file
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Key reference
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Title
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Crystal structure and activity of bacillus subtilis yoaj (exlx1), A bacterial expansin that promotes root colonization.
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Authors
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F.Kerff,
A.Amoroso,
R.Herman,
E.Sauvage,
S.Petrella,
P.Filée,
P.Charlier,
B.Joris,
A.Tabuchi,
N.Nikolaidis,
D.J.Cosgrove.
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Ref.
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Proc Natl Acad Sci U S A, 2008,
105,
16876-16881.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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