5ZH8

Crystal Structure of FmtA from Staphylococcus aureus at 2.58 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Repurposing an Ancient Protein Core Structure: Structural Studies on FmtA, a Novel Esterase of Staphylococcus aureus.

Dalal, V.Kumar, P.Rakhaminov, G.Qamar, A.Fan, X.Hunter, H.Tomar, S.Golemi-Kotra, D.Kumar, P.

(2019) J.Mol.Biol. 431: 3107-3123

  • DOI: 10.1016/j.jmb.2019.06.019

  • PubMed Abstract: 
  • FmtA is a penicillin-recognizing protein (PRP) with novel hydrolytic activity toward the ester bond between d-Ala and the backbone of teichoic acids. Teichoic acids are polyol-phosphate polymers found in the Staphylococcus aureus cell wall, and they ...

    FmtA is a penicillin-recognizing protein (PRP) with novel hydrolytic activity toward the ester bond between d-Ala and the backbone of teichoic acids. Teichoic acids are polyol-phosphate polymers found in the Staphylococcus aureus cell wall, and they play important roles in antibiotic resistance and pathogenesis. Two of the PRPs conserved motifs, namely, SXXK and Y(S)XN, are involved in the hydrolysis by FmtA, but the catalytic mechanism remains elusive. Here we determined the crystal structure of FmtA. FmtA shares the core structure of PRPs: an all α-helical domain and α/β domain sandwiched together. However, it does not have the typical PRPs active-site cleft. Its active site is shallow, solvent-exposed, and enlarged. Furthermore, our mutagenesis and kinetic studies suggest that the SXXK and Y(S)XN motifs of FmtA offer all that is necessary for catalysis, and more: the active-site nucleophile (serine), the general base (lysine) required for the acylation step and the deacylation step, and an anchor (tyrosine) to hold the active-site serine, and possibly the substrate, in an optimum conformation for catalysis. Our study establishes that the FmtA esterase activity represents an expansion of the catalytic activity repertoire of the PRPs core structure, which typically displays peptidase activity. This finding points toward a novel mechanism of ester bond hydrolysis by a PRP. The structure of FmtA provides insights to the design of inhibitor molecules with the potential to serve as leads in the development of novel antibacterial chemotherapeutic agents.


    Organizational Affiliation

    Department of Biotechnology, IIT, Roorkee, Uttrakhand-247667, India.,Department of Biology, York University, 4700 Keele Street, Toronto, Canada. Electronic address: dgkotra@yorku.ca.,Department of Biotechnology, IIT, Roorkee, Uttrakhand-247667, India. Electronic address: kumarfbs@iitr.ac.in.,Department of Biology, York University, 4700 Keele Street, Toronto, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein FmtA
A, B
397Staphylococcus aureusMutation(s): 0 
Gene Names: fmtA (fmt)
Find proteins for O50608 (Staphylococcus aureus)
Go to UniProtKB:  O50608
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 105.391α = 90.00
b = 128.234β = 90.00
c = 107.599γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
BALBESphasing
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-08-28
    Type: Data collection, Database references