Crystal structure of Staphylococcus aureus metallopeptidase (Sapep/DapE) in the apo-form

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1074/jbc.M110.147579
  • Primary Citation of Related Structures:  
    3KHX, 3KHZ, 3KI9

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative dipeptidase SACOL1801
A, B
492Staphylococcus aureus subsp. aureus COLMutation(s): 0 
Gene Names: dipeptidase PepV(SACOL1801)
EC: 3.4.13
Find proteins for Q5HF23 (Staphylococcus aureus (strain COL))
Explore Q5HF23 
Go to UniProtKB:  Q5HF23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HF23
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.823α = 90
b = 134.172β = 94.52
c = 68.282γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-09-28
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description