4Q7O

The crystal structure of an immunity protein NMB0503 from Neisseria meningitidis MC58

Summary for 4Q7O

• Entry DOI: 10.2210/pdb4q7o/pdb
• Descriptor: Immunity protein, BROMIDE ION, FORMIC ACID, ... (4 entities in total)
• Functional Keywords: structural genomics, psi-biology, protein structure initiative, mcsg, midwest center for structural genomics, structure-function analysis of polymorphic cdi toxin-immunity protein complexes, uc4cdi, immune system
• Biological source: Neisseria meningitidis
• Total number of polymer chains: 2
• Total formula weight: 35129.07

Authors

Tan, K.,Stols, L.,Eschenfeldt, W.,Babnigg, G.,Low, D.A.,Hayes, C.S.,Goulding, C.W.,Joachimiak, A.,Midwest Center for Structural Genomics (MCSG),Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI) (deposition date: 2014-04-25, release date: 2014-05-14, Last modification date: 2024-02-28)

Primary citation

Tan, K.,Johnson, P.M.,Stols, L.,Boubion, B.,Eschenfeldt, W.,Babnigg, G.,Hayes, C.S.,Joachimiak, A.,Goulding, C.W.
The structure of a contact-dependent growth-inhibition (CDI) immunity protein from Neisseria meningitidis MC58.
Acta Crystallogr F Struct Biol Commun, 71:702-709, 2015

PubMed Abstract: Contact-dependent growth inhibition (CDI) is an important mechanism of intercellular competition between neighboring Gram-negative bacteria. CDI systems encode large surface-exposed CdiA effector proteins that carry a variety of C-terminal toxin domains (CdiA-CTs). All CDI(+) bacteria also produce CdiI immunity proteins that specifically bind to the cognate CdiA-CT and neutralize its toxin activity to prevent auto-inhibition. Here, the X-ray crystal structure of a CdiI immunity protein from Neisseria meningitidis MC58 is presented at 1.45 Å resolution. The CdiI protein has structural homology to the Whirly family of RNA-binding proteins, but appears to lack the characteristic nucleic acid-binding motif of this family. Sequence homology suggests that the cognate CdiA-CT is related to the eukaryotic EndoU family of RNA-processing enzymes. A homology model is presented of the CdiA-CT based on the structure of the XendoU nuclease from Xenopus laevis. Molecular-docking simulations predict that the CdiA-CT toxin active site is occluded upon binding to the CdiI immunity protein. Together, these observations suggest that the immunity protein neutralizes toxin activity by preventing access to RNA substrates.

PubMed: 26057799
DOI: 10.1107/S2053230X15006585

Experimental method

X-RAY DIFFRACTION (1.45 Å)