Structural basis of inactivation of Ras and Rap1 small GTPases by Ras/Rap1-specific endopeptidase from the sepsis-causing pathogen Vibrio vulnificus

J Biol Chem. 2018 Nov 23;293(47):18110-18122. doi: 10.1074/jbc.RA118.004857. Epub 2018 Oct 3.

Abstract

Multifunctional autoprocessing repeats-in-toxin (MARTX) toxins are secreted by Gram-negative bacteria and function as primary virulence-promoting macromolecules that deliver multiple cytopathic and cytotoxic effector domains into the host cytoplasm. Among these effectors, Ras/Rap1-specific endopeptidase (RRSP) catalyzes the sequence-specific cleavage of the Switch I region of the cellular substrates Ras and Rap1 that are crucial for host innate immune defenses during infection. To dissect the molecular basis underpinning RRSP-mediated substrate inactivation, we determined the crystal structure of an RRSP from the sepsis-causing bacterial pathogen Vibrio vulnificus (VvRRSP). Structural and biochemical analyses revealed that VvRRSP is a metal-independent TIKI family endopeptidase composed of an N-terminal membrane-localization and substrate-recruitment domain (N lobe) connected via an inter-lobe linker to the C-terminal active site-coordinating core β-sheet-containing domain (C lobe). Structure-based mutagenesis identified the 2His/2Glu catalytic residues in the core catalytic domain that are shared with other TIKI family enzymes and that are essential for Ras processing. In vitro KRas cleavage assays disclosed that deleting the N lobe in VvRRSP causes complete loss of enzymatic activity. Endogenous Ras cleavage assays combined with confocal microscopy analysis of HEK293T cells indicated that the N lobe functions both in membrane localization via the first α-helix and in substrate assimilation by altering the functional conformation of the C lobe to facilitate recruitment of cellular substrates. Collectively, these results indicate that RRSP is a critical virulence factor that robustly inactivates Ras and Rap1 and augments the pathogenicity of invading bacteria via the combined effects of its N and C lobes.

Keywords: MARTX toxin; Ras/Rap1-specific endopeptidase; Vibrio vulnificus; bacterial pathogenesis; effector; host–pathogen interaction; sepsis; toxin; virulence factor.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Bacterial Toxins
  • Endopeptidases / chemistry
  • Endopeptidases / genetics
  • Endopeptidases / metabolism*
  • HEK293 Cells
  • Host-Pathogen Interactions
  • Humans
  • Protein Domains
  • Proto-Oncogene Proteins p21(ras) / chemistry
  • Proto-Oncogene Proteins p21(ras) / genetics
  • Proto-Oncogene Proteins p21(ras) / metabolism*
  • Sepsis / enzymology*
  • Sepsis / genetics
  • Sepsis / microbiology*
  • Vibrio vulnificus / chemistry
  • Vibrio vulnificus / enzymology*
  • Vibrio vulnificus / genetics
  • rap1 GTP-Binding Proteins / chemistry
  • rap1 GTP-Binding Proteins / genetics
  • rap1 GTP-Binding Proteins / metabolism*

Substances

  • Bacterial Proteins
  • Bacterial Toxins
  • KRAS protein, human
  • Endopeptidases
  • Proto-Oncogene Proteins p21(ras)
  • rap1 GTP-Binding Proteins

Associated data

  • PDB/2N9W
  • PDB/4ERR
  • PDB/2EBF
  • PDB/5T09
  • PDB/3B55
  • PDB/2G5G
  • PDB/5W22
  • PDB/4DSO
  • PDB/6A8J
  • PDB/6A7H