3M6R

Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) G41M mutant in complex with actinonin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis

Fieulaine, S.Boularot, A.Artaud, I.Desmadril, M.Dardel, F.Meinnel, T.Giglione, C.

(2011) Plos Biol. 9: e1001066-e1001066

  • DOI: 10.1371/journal.pbio.1001066
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to ali ...

    For several decades, molecular recognition has been considered one of the most fundamental processes in biochemistry. For enzymes, substrate binding is often coupled to conformational changes that alter the local environment of the active site to align the reactive groups for efficient catalysis and to reach the transition state. Adaptive substrate recognition is a well-known concept; however, it has been poorly characterized at a structural level because of its dynamic nature. Here, we provide a detailed mechanism for an induced-fit process at atomic resolution. We take advantage of a slow, tight binding inhibitor-enzyme system, actinonin-peptide deformylase. Crystal structures of the initial open state and final closed state were solved, as well as those of several intermediate mimics captured during the process. Ligand-induced reshaping of a hydrophobic pocket drives closure of the active site, which is finally "zipped up" by additional binding interactions. Together with biochemical analyses, these data allow a coherent reconstruction of the sequence of events leading from the encounter complex to the key-lock binding state of the enzyme. A "movie" that reconstructs this entire process can be further extrapolated to catalysis.


    Organizational Affiliation

    CNRS, ISV, UPR2355, Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase 1B
A, B, C, D
193Arabidopsis thalianaMutation(s): 1 
Gene Names: PDF1B (DEF2)
EC: 3.5.1.88
Find proteins for Q9FUZ2 (Arabidopsis thaliana)
Go to UniProtKB:  Q9FUZ2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BB2Kd: 32 nM BINDINGMOAD
BB2Kd: 32 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.640α = 90.00
b = 66.730β = 90.00
c = 189.690γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-03-21
    Type: Database references