4H0F

Mutant Structure of laminin-binding adhesin (Lmb) from Streptococcus agalactiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Metal binding is critical for the folding and function of laminin binding protein, Lmb of Streptococcus agalactiae.

Ragunathan, P.Sridaran, D.Weigel, A.Shabayek, S.Spellerberg, B.Ponnuraj, K.

(2013) Plos One 8: e67517-e67517

  • DOI: 10.1371/journal.pone.0067517

  • PubMed Abstract: 
  • Lmb is a 34 kDa laminin binding surface adhesin of Streptococcus agalactiae. The structure of Lmb reported by us recently has shown that it consists of a metal binding crevice, in which a zinc ion is coordinated to three highly conserved histidines. ...

    Lmb is a 34 kDa laminin binding surface adhesin of Streptococcus agalactiae. The structure of Lmb reported by us recently has shown that it consists of a metal binding crevice, in which a zinc ion is coordinated to three highly conserved histidines. To elucidate the structural and functional significance of the metal ion in Lmb, these histidines have been mutated to alanine and single, double and triple mutants were generated. These mutations resulted in insolubility of the protein and revealed altered secondary and tertiary structures, as evidenced by circular dichroism and fluorescence spectroscopy studies. The mutations also significantly decreased the binding affinity of Lmb to laminin, implicating the role played by the metal binding residues in maintaining the correct conformation of the protein for its binding to laminin. A highly disordered loop, proposed to be crucial for metal acquisition in homologous structures, was deleted in Lmb by mutation (ΔLmb) and its crystal structure was solved at 2.6 Å. The ΔLmb structure was identical to the native Lmb structure with a bound zinc ion and exhibited laminin binding activity similar to wild type protein, suggesting that the loop might not have an important role in metal acquisition or adhesion in Lmb. Targeted mutations of histidine residues confirmed the importance of the zinc binding crevice for the structure and function of the Lmb adhesin.


    Organizational Affiliation

    Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Laminin-binding surface protein
A, B
264Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)Mutation(s): 0 
Gene Names: lmb
Find proteins for Q8DZ80 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R))
Go to UniProtKB:  Q8DZ80
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.400α = 90.00
b = 93.990β = 105.42
c = 66.880γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
XRD1data collection
CNSrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-09-11
    Type: Database references
  • Version 1.2: 2015-07-29
    Type: Other