Crystal Structure Analysis of double cysteine mutant of S.epidermidis adhesin SdrG: Evidence for the Dock,Lock and Latch ligand binding mechanism

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Evidence for the "dock, lock, and latch" ligand binding mechanism of the staphylococcal microbial surface component recognizing adhesive matrix molecules (MSCRAMM) SdrG.

Bowden, M.G.Heuck, A.P.Ponnuraj, K.Kolosova, E.Choe, D.Gurusiddappa, S.Narayana, S.V.Johnson, A.E.Hook, M.

(2008) J Biol Chem 283: 638-647

  • DOI: https://doi.org/10.1074/jbc.M706252200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Staphylococcus epidermidis is an opportunistic pathogen and a major cause of foreign body infections. The S. epidermidis fibrinogen (Fg)-binding adhesin SdrG is necessary and sufficient for the attachment of this pathogen to Fg-coated materials. Based largely on structural analyses of the ligand binding domain of SdrG as an apo-protein and in complex with a Fg-like peptide, we proposed that SdrG follows a "dock, lock, and latch" mechanism to bind to Fg. This binding mechanism involves the docking of the ligand in a pocket formed between two SdrG subdomains followed by the movement of a C-terminal extension of one subdomain to cover the ligand and to insert and complement a beta-sheet in a neighboring subdomain. These proposed events result in a greatly stabilized closed conformation of the MSCRAMM-ligand complex. In this report, we describe a biochemical analysis of the proposed conformational changes that SdrG undergoes upon binding to its ligand. We have introduced disulfide bonds into SdrG to stabilize the open and closed forms of the apo-form of the MSCRAMM. We show that the stabilized closed form does not bind to the ligand and that binding can be restored in the presence of reducing agents such as dithiothreitol. We have also used Förster resonance energy transfer to dynamically show the conformational changes of SdrG upon binding to its ligand. Finally, we have used isothermic calorimetry to determine that hydrophobic interactions between the ligand and the protein are responsible for re-directing the C-terminal extension of the second subdomain required for triggering the beta-strand complementation event.

  • Organizational Affiliation

    Center for Extracellular Matrix Biology, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Houston, Texas 77030. Electronic address: gbowden@ibt.tamhsc.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine-aspartate repeat-containing protein G
A, B
340Staphylococcus epidermidisMutation(s): 2 
Gene Names: SdrG
Find proteins for Q9KI13 (Staphylococcus epidermidis)
Explore Q9KI13 
Go to UniProtKB:  Q9KI13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KI13
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.507α = 90
b = 94.172β = 90
c = 129.583γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-31
    Changes: Experimental preparation
  • Version 1.3: 2021-10-20
    Changes: Database references
  • Version 1.4: 2023-08-30
    Changes: Data collection, Refinement description