2HPO

Structure of Aminopeptidase N from E. coli Suggests a Compartmentalized, Gated Active Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of aminopeptidase N from Escherichia coli suggests a compartmentalized, gated active site.

Addlagatta, A.Gay, L.Matthews, B.W.

(2006) Proc.Natl.Acad.Sci.Usa 103: 13339-13344

  • DOI: 10.1073/pnas.0606167103
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aminopeptidase N from Escherichia coli is a major metalloprotease that participates in the controlled hydrolysis of peptides in the proteolytic pathway. Determination of the 870-aa structure reveals that it has four domains similar to the tricorn-int ...

    Aminopeptidase N from Escherichia coli is a major metalloprotease that participates in the controlled hydrolysis of peptides in the proteolytic pathway. Determination of the 870-aa structure reveals that it has four domains similar to the tricorn-interacting factor F3. The thermolysin-like active site is enclosed within a large cavity with a volume of 2,200 A(3), which is inaccessible to substrates except for a small opening of approximately 8-10 A. The substrate-based inhibitor bestatin binds to the protein with minimal changes, suggesting that this is the active form of the enzyme. The previously described structure of F3 had three distinct conformations that were described as "closed," "intermediate," and "open." The structure of aminopeptidase N from E. coli, however, is substantially more closed than any of these. Taken together, the results suggest that these proteases, which are involved in intracellular peptide degradation, prevent inadvertent hydrolysis of inappropriate substrates by enclosing the active site within a large cavity. There is also some evidence that the open form of the enzyme, which admits substrates, remains inactive until it adopts the closed form.


    Organizational Affiliation

    Howard Hughes Medical Institute and Institute of Molecular Biology and Department of Physics, University of Oregon, Eugene, OR 97403-1229.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminopeptidase N
A
891Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pepN
EC: 3.4.11.2
Find proteins for P04825 (Escherichia coli (strain K12))
Go to UniProtKB:  P04825
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.157 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 120.438α = 90.00
b = 120.438β = 90.00
c = 170.561γ = 120.00
Software Package:
Software NamePurpose
SHELXSphasing
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance