6QBE

Crystal structure of non-toxic HaNLP3 protein

Summary for 6QBE

• Entry DOI: 10.2210/pdb6qbe/pdb
• Descriptor: Nep1-like protein, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: non-toxic nlp protein, beta-sandwich, hyaloperonospora arabidopsidis, toxin
• Biological source: Hyaloperonospora arabidopsidis
• Total number of polymer chains: 1
• Total formula weight: 29285.22

Authors

Lenarcic, T.,Podobnik, M.,Anderluh, G. (deposition date: 2018-12-21, release date: 2019-08-28, Last modification date: 2024-01-24)

Primary citation

Lenarcic, T.,Pirc, K.,Hodnik, V.,Albert, I.,Borisek, J.,Magistrato, A.,Nurnberger, T.,Podobnik, M.,Anderluh, G.
Molecular basis for functional diversity among microbial Nep1-like proteins.
Plos Pathog., 15:e1007951-e1007951, 2019

PubMed Abstract: Necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are secreted by several phytopathogenic microorganisms. They trigger necrosis in various eudicot plants upon binding to plant sphingolipid glycosylinositol phosphorylceramides (GIPC). Interestingly, HaNLP3 from the obligate biotroph oomycete Hyaloperonospora arabidopsidis does not induce necrosis. We determined the crystal structure of HaNLP3 and showed that it adopts the NLP fold. However, the conformations of the loops surrounding the GIPC headgroup-binding cavity differ from those of cytotoxic Pythium aphanidermatum NLPPya. Essential dynamics extracted from μs-long molecular dynamics (MD) simulations reveals a limited conformational plasticity of the GIPC-binding cavity in HaNLP3 relative to toxic NLPs. This likely precludes HaNLP3 binding to GIPCs, which is the underlying reason for the lack of toxicity. This study reveals that mutations at key protein regions cause a switch between non-toxic and toxic phenotypes within the same protein scaffold. Altogether, these data provide evidence that protein flexibility is a distinguishing trait of toxic NLPs and highlight structural determinants for a potential functional diversification of non-toxic NLPs utilized by biotrophic plant pathogens.

PubMed: 31479498
DOI: 10.1371/journal.ppat.1007951

Experimental method

X-RAY DIFFRACTION (2 Å)