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6QBD

Crystal structure of NLPPya P41A, D44N, N48E mutant

Summary for 6QBD
Entry DOI10.2210/pdb6qbd/pdb
Descriptor25 kDa protein elicitor, MAGNESIUM ION (3 entities in total)
Functional Keywordsnlp protein, mutant, beta-sandwich, pythium aphanidermatum, toxin
Biological sourcePythium aphanidermatum
Total number of polymer chains2
Total formula weight46656.71
Authors
Lenarcic, T.,Podobnik, M.,Anderluh, G. (deposition date: 2018-12-21, release date: 2019-08-28, Last modification date: 2024-11-13)
Primary citationLenarcic, 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
Cited by
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
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (1.95 Å)
Structure validation

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数据于2025-06-25公开中

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