3BF0

Crystal structure of Escherichia coli Signal peptide peptidase (SppA), Native crystals


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a bacterial signal Peptide peptidase.

Kim, A.C.Oliver, D.C.Paetzel, M.

(2008) J.Mol.Biol. 376: 352-366

  • DOI: 10.1016/j.jmb.2007.11.080
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Signal peptide peptidase (Spp) is the enzyme responsible for cleaving the remnant signal peptides left behind in the membrane following Sec-dependent protein secretion. Spp activity appears to be present in all cell types, eukaryotic, prokaryotic and ...

    Signal peptide peptidase (Spp) is the enzyme responsible for cleaving the remnant signal peptides left behind in the membrane following Sec-dependent protein secretion. Spp activity appears to be present in all cell types, eukaryotic, prokaryotic and archaeal. Here we report the first structure of a signal peptide peptidase, that of the Escherichia coli SppA (SppA(EC)). SppA(EC) forms a tetrameric assembly with a novel bowl-shaped architecture. The bowl has a dramatically hydrophobic interior and contains four separate active sites that utilize a Ser/Lys catalytic dyad mechanism. Our structural analysis of SppA reveals that while in many Gram-negative bacteria as well as characterized plant variants, a tandem duplication in the protein fold creates an intact active site at the interface between the repeated domains, other species, particularly Gram-positive and archaeal organisms, encode half-size, unduplicated SppA variants that could form similar oligomers to their duplicated counterparts, but using an octamer arrangement and with the catalytic residues provided by neighboring monomers. The structure reveals a similarity in the protein fold between the domains in the periplasmic Ser/Lys protease SppA and the monomers seen in the cytoplasmic Ser/His/Asp protease ClpP. We propose that SppA may, in addition to its role in signal peptide hydrolysis, have a role in the quality assurance of periplasmic and membrane-bound proteins, similar to the role that ClpP plays for cytoplasmic proteins.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building, 8888 University Drive, Burnaby, British Columbia, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease 4
A, B, C, D
593Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: sppA
EC: 3.4.21.-
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Peptidases
Protein: 
Signal Peptide Peptidase (SppA), native protein
Find proteins for P08395 (Escherichia coli (strain K12))
Go to UniProtKB:  P08395
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 94.171α = 90.00
b = 153.485β = 104.25
c = 100.659γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-11-20 
  • Released Date: 2007-12-18 
  • Deposition Author(s): Paetzel, M.

Revision History 

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description