4Q4I

Crystal structure of E.coli aminopeptidase N in complex with amastatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for the inhibition of M1 family aminopeptidases by the natural product actinonin: Crystal structure in complex with E. coli Aminopeptidase N

Ganji, R.J.Reddi, R.Gumpena, R.Marapaka, A.K.Arya, T.Sankoju, P.Bhukya, S.Addlagatta, A.

(2015) Protein Sci. --: --

  • DOI: 10.1002/pro.2653
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Actinonin is a pseudotripeptide that displays a high affinity towards metalloproteases including peptide deformylases (PDFs) and M1 family aminopeptidases. PDF and M1 family aminopeptidases belong to thermolysin-metzincin superfamily. One of the majo ...

    Actinonin is a pseudotripeptide that displays a high affinity towards metalloproteases including peptide deformylases (PDFs) and M1 family aminopeptidases. PDF and M1 family aminopeptidases belong to thermolysin-metzincin superfamily. One of the major differences in terms of substrate binding pockets between these families is presence (in M1 aminopeptidases) or absence (in PDFs) of an S1 substrate pocket. The binding mode of actinonin to PDFs has been established previously; however, it is not clear how the actinonin, without a P1 residue, would bind to the M1 aminopeptidases. Here we describe the crystal structure of Escherichia coli aminopeptidase N (ePepN), a model protein of the M1 family aminopeptidases in complex with actinonin. For comparison we have also determined the structure of ePepN in complex with a well-known tetrapeptide inhibitor, amastatin. From the comparison of the actinonin and amastatin ePepN complexes, it is clear that the P1 residue is not critical as long as strong metal chelating head groups, like hydroxamic acid or α-hydroxy ketone, are present. Results from this study will be useful for the design of selective and efficient hydroxamate inhibitors against M1 family aminopeptidases.


    Organizational Affiliation

    Center for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, Telangana, India.




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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Amastatin
C
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 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
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000415
Query on PRD_000415
CAmastatinPeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.140 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.386α = 90.00
b = 119.386β = 90.00
c = 170.129γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
ADSCdata collection
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-15
    Type: Initial release