3G5K

Structure and activity of human mitochondrial peptide deformylase, a novel cancer target


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and activity of human mitochondrial peptide deformylase, a novel cancer target

Escobar-Alvarez, S.Goldgur, Y.Yang, G.Ouerfelli, O.Li, Y.Scheinberg, D.A.

(2009) J.Mol.Biol. 387: 1211-1228

  • DOI: 10.1016/j.jmb.2009.02.032
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Peptide deformylase proteins (PDFs) participate in the N-terminal methionine excision pathway of newly synthesized peptides. We show that the human PDF (HsPDF) can deformylate its putative substrates derived from mitochondrial DNA-encoded proteins. T ...

    Peptide deformylase proteins (PDFs) participate in the N-terminal methionine excision pathway of newly synthesized peptides. We show that the human PDF (HsPDF) can deformylate its putative substrates derived from mitochondrial DNA-encoded proteins. The first structural model of a mammalian PDF (1.7 A), HsPDF, shows a dimer with conserved topology of the catalytic residues and fold as non-mammalian PDFs. The HsPDF C-terminus topology and the presence of a helical loop (H2 and H3), however, shape a characteristic active site entrance. The structure of HsPDF bound to the peptidomimetic inhibitor actinonin (1.7 A) identified the substrate-binding site. A defined S1' pocket, but no S2' or S3' substrate-binding pockets, exists. A conservation of PDF-actinonin interaction across PDFs was observed. Despite the lack of true S2' and S3' binding pockets, confirmed through peptide binding modeling, enzyme kinetics suggest a combined contribution from P2'and P3' positions of a formylated peptide substrate to turnover.


    Organizational Affiliation

    Molecular Pharmacology and Chemistry Program, Sloan-Kettering Institute, 415 E. 68th Street Zuckerman Z1941, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase, mitochondrial
A, B, C, D
183Homo sapiensMutation(s): 0 
Gene Names: PDF (PDF1A)
EC: 3.5.1.88
Find proteins for Q9HBH1 (Homo sapiens)
Go to Gene View: PDF
Go to UniProtKB:  Q9HBH1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BB2
Query on BB2

Download SDF File 
Download CCD File 
A, B, C, D
ACTINONIN
2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE
C19 H35 N3 O5
XJLATMLVMSFZBN-VYDXJSESSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A, B, C, D
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BB2IC50: 1.5 - 2700 nM (100) BINDINGDB
BB2Ki: 0.3 nM (100) BINDINGDB
BB2Ki: 0.3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 116.144α = 90.00
b = 77.830β = 107.46
c = 110.532γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
ADSCdata collection
AMoREphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance