4ICS

Crystal structure of PepS from Streptococcus pneumoniae in complex with a substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure-based elucidation of the regulatory mechanism for aminopeptidase activity.

Ta, H.M.Bae, S.Han, S.Song, J.Ahn, T.K.Hohng, S.Lee, S.Kim, K.K.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1738-1747

  • DOI: 10.1107/S0907444913012651
  • Primary Citation of Related Structures:  
    4ICQ, 4ICR, 4ICS

  • PubMed Abstract: 
  • The specificity of proteases for the residues in and length of substrates is key to understanding their regulatory mechanism, but little is known about length selectivity. Crystal structure analyses of the bacterial aminopeptidase PepS, combined with functional and single-molecule FRET assays, have elucidated a molecular basis for length selectivity ...

    The specificity of proteases for the residues in and length of substrates is key to understanding their regulatory mechanism, but little is known about length selectivity. Crystal structure analyses of the bacterial aminopeptidase PepS, combined with functional and single-molecule FRET assays, have elucidated a molecular basis for length selectivity. PepS exists in open and closed conformations. Substrates can access the binding hole in the open conformation, but catalytic competency is only achieved in the closed conformation by formation of the S1 binding pocket and proximal movement of Glu343, a general base, to the cleavage site. Hence, peptides longer than the depth of the binding hole block the transition from the open to the closed conformation, and thus length selection is a prerequisite for catalytic activation. A triple-sieve interlock mechanism is proposed featuring the coupling of length selectivity with residue specificity and active-site positioning.


    Organizational Affiliation

    Department of Molecular Cell Biology, School of Medicine, Samsung Biomedical Research Institute, Sungkyunkwan University, Suwon 440-746, Republic of Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminopeptidase PepSA, B413Streptococcus pneumoniae TIGR4Mutation(s): 1 
Gene Names: pepSSP_0278
EC: 3.4.11
Find proteins for A0A0H2UN95 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore A0A0H2UN95 
Go to UniProtKB:  A0A0H2UN95
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.365α = 90
b = 126.365β = 90
c = 139.328γ = 90
Software Package:
Software NamePurpose
EPMRphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release