4WVG

Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Peptide binding to a bacterial signal peptidase visualized by peptide tethering and carrier-driven crystallization.

Ting, Y.T.Harris, P.W.Batot, G.Brimble, M.A.Baker, E.N.Young, P.G.

(2016) IUCrJ 3: 10-19

  • DOI: 10.1107/S2052252515019971
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial type I signal peptidases (SPases) are membrane-anchored serine proteases that process the signal peptides of proteins exported via the Sec and Tat secretion systems. Despite their crucial importance for bacterial virulence and their attract ...

    Bacterial type I signal peptidases (SPases) are membrane-anchored serine proteases that process the signal peptides of proteins exported via the Sec and Tat secretion systems. Despite their crucial importance for bacterial virulence and their attractiveness as drug targets, only one such enzyme, LepB from Escherichia coli, has been structurally characterized, and the transient nature of peptide binding has stymied attempts to directly visualize SPase-substrate complexes. Here, the crystal structure of SpsB, the type I signal peptidase from the Gram-positive pathogen Staphylococcus aureus, is reported, and a peptide-tethering strategy that exploits the use of carrier-driven crystallization is described. This enabled the determination of the crystal structures of three SpsB-peptide complexes, both with cleavable substrates and with an inhibitory peptide. SpsB-peptide interactions in these complexes are almost exclusively limited to the canonical signal-peptide motif Ala-X-Ala, for which clear specificity pockets are found. Minimal contacts are made outside this core, with the variable side chains of the peptides accommodated in shallow grooves or exposed faces. These results illustrate how high fidelity is retained despite broad sequence diversity, in a process that is vital for cell survival.


    Organizational Affiliation

    School of Biological Sciences, The University of Auckland, Auckland 1142, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1142, New Zealand.,School of Biological Sciences, The University of Auckland , Auckland 1142, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1142, New Zealand; School of Chemical Sciences, The University of Auckland, Auckland 1142, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein,Signal peptidase IB
A
542Escherichia coli O157:H7Staphylococcus aureus (strain COL)
This entity is chimeric
Mutation(s): 1 
Gene Names: malE, spsB
EC: 3.4.21.89
Membrane protein
mpstruct
Group: 
MONOTOPIC MEMBRANE PROTEINS
Sub Group: 
Peptidases
Protein: 
SpsB Signal Peptidase (SPase), apoprotein
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AEY0
Find proteins for Q5HHB9 (Staphylococcus aureus (strain COL))
Go to UniProtKB:  Q5HHB9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.683α = 90.00
b = 63.565β = 92.59
c = 79.892γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata scaling
PDB_EXTRACTdata extraction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Health Research CouncilNew Zealand--

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2018-04-25
    Type: Data collection, Database references
  • Version 1.4: 2018-06-13
    Type: Data collection
  • Version 1.5: 2019-01-23
    Type: Data collection, Source and taxonomy