3KI9

Crystal structure of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the Mn2+ bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Staphylococcus aureus metallopeptidase (Sapep) reveals large domain motions between the manganese-bound and apo-states

Girish, T.S.Gopal, B.

(2010) J.Biol.Chem. 285: 29406-29415

  • DOI: 10.1074/jbc.M110.147579
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Proteases belonging to the M20 family are characterized by diverse substrate specificity and participate in several metabolic pathways. The Staphylococcus aureus metallopeptidase, Sapep, is a member of the aminoacylase-I/M20 protein family. This prot ...

    Proteases belonging to the M20 family are characterized by diverse substrate specificity and participate in several metabolic pathways. The Staphylococcus aureus metallopeptidase, Sapep, is a member of the aminoacylase-I/M20 protein family. This protein is a Mn(2+)-dependent dipeptidase. The crystal structure of this protein in the Mn(2+)-bound form and in the open, metal-free state suggests that large interdomain movements could potentially regulate the activity of this enzyme. We note that the extended inactive conformation is stabilized by a disulfide bond in the vicinity of the active site. Although these cysteines, Cys(155) and Cys(178), are not active site residues, the reduced form of this enzyme is substantially more active as a dipeptidase. These findings acquire further relevance given a recent observation that this enzyme is only active in methicillin-resistant S. aureus. The structural and biochemical features of this enzyme provide a template for the design of novel methicillin-resistant S. aureus-specific therapeutics.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative dipeptidase SACOL1801
A
492Staphylococcus aureus (strain COL)Mutation(s): 0 
EC: 3.4.13.-
Find proteins for Q5HF23 (Staphylococcus aureus (strain COL))
Go to UniProtKB:  Q5HF23
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.202 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 158.150α = 90.00
b = 158.150β = 90.00
c = 158.150γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PHASERphasing
MOSFLMdata reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-09-28
    Type: Database references