2CBM

Crystal structure of the apo-form of a neocarzinostatin mutant evolved to bind testosterone.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of in Vitro Evolved Binding Sites on Neocarzinostatin Scaffold Reveal Unanticipated Evolutionary Pathways.

Drevelle, A.Graille, M.Heyd, B.Sorel, I.Ulryck, N.Pecorari, F.Desmadril, M.Van Tilbeurgh, H.Minard, P.

(2006) J Mol Biol 358: 455

  • DOI: 10.1016/j.jmb.2006.02.002
  • Primary Citation of Related Structures:  
    2CBO, 2CBM, 2CBT, 2CBQ

  • PubMed Abstract: 
  • We have recently applied in vitro evolution methods to create in Neocarzinostatin a new binding site for a target molecule unrelated to its natural ligand. The main objective of this work was to solve the structure of some of the selected binders in complex with the target molecule: testosterone ...

    We have recently applied in vitro evolution methods to create in Neocarzinostatin a new binding site for a target molecule unrelated to its natural ligand. The main objective of this work was to solve the structure of some of the selected binders in complex with the target molecule: testosterone. Three proteins (1a.15, 3.24 and 4.1) were chosen as representative members of sequence families that came out of the selection process within different randomization schemes. In order to evaluate ligand-induced conformational adaptation, we also determined the structure of one of the proteins (3.24) in the free and complexed forms. Surprisingly, all these mutants bind not one but two molecules of testosterone in two very different ways. The 3.24 structure revealed that the protein spontaneously evolved in the system to bind two ligand molecules in one single binding crevice. These two binding sites are formed by substituted as well as by non-variable side-chains. The comparison with the free structure shows that only limited structural changes are observed upon ligand binding. The X-ray structures of the complex formed by 1a.15 and 4.1 Neocarzinostatin mutants revealed that the two variants form very similar dimers. These dimers were observed neither for the uncomplexed variants nor for wild-type Neocarzinostatin but were shown here to be induced by ligand binding. Comparison of the three complexed forms clearly suggests that these unanticipated structural responses resulted from the molecular arrangement used for the selection experiments.


    Related Citations: 
    • In Vitro Evolution of the Binding Specificity of Neocarzinostatin, an Enediyne-Binding Chromoprotein.
      Heyd, B., Pecorari, F., Collinet, B., Adjadj, E., Desmadril, M., Minard, P.
      (2003) Biochemistry 42: 5674

    Organizational Affiliation

    Equipe de Modélisation et Ingénierie des Protéines, IBBMC, CNRS, UMR8619, Université Paris XI, Bât. 430, 91405 Orsay, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NEOCARZINOSTATIN A112Streptomyces carzinostaticusMutation(s): 7 
Gene Names: ncsA
Find proteins for P0A3R9 (Streptomyces carzinostaticus)
Explore P0A3R9 
Go to UniProtKB:  P0A3R9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.125α = 90
b = 60.125β = 90
c = 97.004γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-22
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance