6Q24

Structure of pro-Esp mutant- S235A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insights into the role of the N-terminus in the activation and function of extracellular serine protease from Staphylococcus epidermidis.

Manne, K.Narayana, S.V.L.

(2020) Acta Crystallogr D Struct Biol 76: 28-40

  • DOI: 10.1107/S2059798319015055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Extracellular serine protease (Esp) from Staphylococcus epidermidis is a glutamyl endopeptidase that inhibits the growth and formation of S. aureus biofilms. Previously, crystal structures of the matured and active Esp have been determined. Interesti ...

    Extracellular serine protease (Esp) from Staphylococcus epidermidis is a glutamyl endopeptidase that inhibits the growth and formation of S. aureus biofilms. Previously, crystal structures of the matured and active Esp have been determined. Interestingly, many of the staphylococcal glutamyl endopeptidase zymogens, including V8 from Staphylococcus aureus and Esp from S. epidermidis, contain unusually long pro-peptide segments; however, their function is not known. With the aim of elucidating the function of these pro-peptide segments, crystal structures of the Esp zymogen (Pro-Esp) and its variants were determined. It was observed that the N-terminus of the Pro-Esp crystal structure is flexible and is not associated with the main body of the enzyme, unlike in the known active Esp structure. In addition, the loops that border the putative substrate-binding pocket of Pro-Esp are flexible and disordered; the structural components that are responsible for enzyme specificity and efficiency in serine proteases are disordered in Pro-Esp. However, the N-terminal locked Pro-Esp variants exhibit a rigid substrate-binding pocket similar to the active Esp structure and regain activity. These structural studies highlight the role of the N-terminus in stabilizing the structural components responsible for the activity and specificity of staphylococcal glutamyl endopeptidases.


    Organizational Affiliation

    Center for Biophysical Sciences and Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutamyl endopeptidase
A
251Staphylococcus epidermidis (strain ATCC 12228)Mutation(s): 1 
Gene Names: gseA (esp)
EC: 3.4.21.19
Find proteins for P0C0Q2 (Staphylococcus epidermidis (strain ATCC 12228))
Go to UniProtKB:  P0C0Q2
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.193 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.100α = 90.00
b = 69.100β = 90.00
c = 127.330γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
XDSdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01- AI106808

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-12-18
    Type: Author supporting evidence
  • Version 1.2: 2020-01-08
    Type: Database references
  • Version 1.3: 2020-01-22
    Type: Database references