4ICQ

Structural basis for substrate recognition and reaction mechanism of bacterial aminopeptidase peps


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 

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.,Sect.D 69: 1738-1747

  • DOI: 10.1107/S0907444913012651
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminopeptidase PepS
A, B
413Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 0 
Gene Names: pepS
EC: 3.4.11.-
Find proteins for A0A0H2UN95 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  A0A0H2UN95
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 126.644α = 90.00
b = 126.644β = 90.00
c = 139.027γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
REFMACrefinement
HKL-2000data reduction
ADSCdata collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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