1FY2

Aspartyl Dipeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad.

Hakansson, K.Wang, A.H.Miller, C.G.

(2000) Proc Natl Acad Sci U S A 97: 14097-14102

  • DOI: 10.1073/pnas.260376797
  • Primary Citation of Related Structures:  
    1FY2, 1FYE

  • PubMed Abstract: 
  • The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E, was solved crystallographically and refined to 1.2-A resolution. The structure of this 25-kDa enzyme consists of two mixed beta-sheets forming a V, flanked by six alpha-helices ...

    The three-dimensional structure of Salmonella typhimurium aspartyl dipeptidase, peptidase E, was solved crystallographically and refined to 1.2-A resolution. The structure of this 25-kDa enzyme consists of two mixed beta-sheets forming a V, flanked by six alpha-helices. The active site contains a Ser-His-Glu catalytic triad and is the first example of a serine peptidase/protease with a glutamate in the catalytic triad. The active site Ser is located on a strand-helix motif reminiscent of that found in alpha/beta-hydrolases, but the polypeptide fold and the organization of the catalytic triad differ from those of the known serine proteases. This enzyme is a member of a family of serine hydrolases and appears to represent a new example of convergent evolution of peptidase activity.


    Related Citations: 
    • Peptidase E, a peptidase specific for N-terminal aspartic dipeptides, is a serine hydrolase
      Lassy, R.A., Miller, C.G.
      (2000) J Bacteriol 182: 2536
    • Cloning and nucleotide sequence of the cyclic AMP receptor protein-regulated Salmonella typhimurium pepE gene and crystallization of its product, an alpha-aspartyl dipeptidase
      Conlin, C.A., Hakansson, K., Liljas, A., Miller, C.G.
      (1994) J Bacteriol 176: 166

    Organizational Affiliation

    Departments of Microbiology and Cell and Structural Biology, B103 Chemical and Life Science Laboratory, University of Illinois at Urbana-Champaign, 601 South Goodwin Avenue, Urbana, IL 61801, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ASPARTYL DIPEPTIDASEA229Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
EC: 3.4 (PDB Primary Data), 3.4.13.21 (UniProt)
Find proteins for P36936 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P36936 
Go to UniProtKB:  P36936
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download Ideal Coordinates CCD File 
B [auth A]CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.986α = 90
b = 42.69β = 106.06
c = 62.496γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-10
    Type: Initial release
  • Version 1.1: 2007-10-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model