1HI9

Zn-dependent D-aminopeptidase DppA from Bacillus subtilis, a self-compartmentalizing protease.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Bacillus Subtilis D-Aminopeptidase Dppa Reveals a Novel Self-Compartmentalizing Protease

Remaut, H.Bompard-Gilles, C.Goffin, C.Frere, J.M.Van Beeumen, J.

(2001) Nat.Struct.Mol.Biol. 8: 674

  • DOI: 10.1038/90380

  • PubMed Abstract: 
  • Bacillus subtilis DppA is a binuclear zinc-dependent, D-specific aminopeptidase. The X-ray structure of the enzyme has been determined at 2.4 A resolution by a three-wavelength MAD experiment. The structure reveals that DppA is a new example of a 'se ...

    Bacillus subtilis DppA is a binuclear zinc-dependent, D-specific aminopeptidase. The X-ray structure of the enzyme has been determined at 2.4 A resolution by a three-wavelength MAD experiment. The structure reveals that DppA is a new example of a 'self-compartmentalizing protease', a family of proteolytic complexes. Proteasomes are the most extensively studied representatives of this family. The DppA enzyme is composed of identical 30 kDa subunits organized in a decamer with 52 point-group symmetry. A 20 A wide channel runs through the complex, giving access to a central chamber holding the active sites. The structure shows DppA to be a prototype of a new family of metalloaminopeptidases characterized by the SXDXEG key sequence.


    Organizational Affiliation

    Laboratory of Protein Biochemistry and Protein Engineering, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIPEPTIDE TRANSPORT PROTEIN DPPA
A, B, C, D, E
274Bacillus subtilis (strain 168)Gene Names: dppA (dciAA)
EC: 3.4.11.-
Find proteins for P26902 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P26902
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.232 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 145.110α = 90.00
b = 165.860β = 90.00
c = 109.930γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
DMphasing
CNSrefinement
SCALEPACKdata scaling
DMphasing
MLPHAREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance