Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with an inhibitor peptide (pep3).

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


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: https://doi.org/10.1107/S2052252515019971
  • Primary Citation of Related Structures:  
    4WVG, 4WVH, 4WVI, 4WVJ

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein,Signal peptidase IB533Escherichia coli K-12Staphylococcus aureus subsp. aureus str. Newman
This entity is chimeric
Mutation(s): 2 
Gene Names: malEZ5632ECs5017spsBSACOL0969
Membrane Entity: Yes 
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q5HHB9 (Staphylococcus aureus (strain COL))
Explore Q5HHB9 
Go to UniProtKB:  Q5HHB9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ5HHB9P0AEX9
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
inhibitor peptide (PEP3)B [auth D]14Staphylococcus aureusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence


Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseC [auth B]2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.11α = 90
b = 80.101β = 90
c = 119.648γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Health Research Council (HRC)New Zealand--

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.3: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.4: 2018-06-13
    Changes: Data collection
  • Version 1.5: 2019-01-23
    Changes: Data collection, Source and taxonomy
  • Version 1.6: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary