1O5P

Solution Structure of holo-Neocarzinostatin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 16000 
  • Conformers Submitted: 60 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution NMR Structure Investigation for Releasing Mechanism of Neocarzinostatin Chromophore from the Holoprotein

Takashima, H.Yoshida, T.Ishino, T.Hasuda, K.Ohkubo, T.Kobayashi, Y.

(2005) J.Biol.Chem. 280: 11340-11346

  • DOI: 10.1074/jbc.M411579200

  • PubMed Abstract: 
  • Holo-neocarzinostatin (holo-NCS) is a complex protein carrying the anti-tumor active enediyne ring chromophore by a scaffold consisting of an immunoglobulin-like seven-stranded anti-parallel beta-barrel. Because of the labile chromophore reflecting i ...

    Holo-neocarzinostatin (holo-NCS) is a complex protein carrying the anti-tumor active enediyne ring chromophore by a scaffold consisting of an immunoglobulin-like seven-stranded anti-parallel beta-barrel. Because of the labile chromophore reflecting its extremely strong DNA cleavage activity and complete stabilization in the complex, holo-NCS has attracted much attention in clinical use as well as for drug delivery systems. Despite many structural analyses for holo-NCS, the chromophore-releasing mechanism to trigger prompt attacks on the target DNA is still unclear. We determined the three-dimensional structure of the protein and the internal motion by multinuclear NMR to investigate the releasing mechanism. The internal motion studied by 13C NMR methine relaxation experiments showed that the complex has a rigid structure for its loops as well as the beta-barrel in aqueous solution. This agrees with the refined NMR solution structure, which has good convergence in the loop regions. We also showed that the chromophore displayed a similar internal motion as the protein moiety. The structural comparison between the refined solution structure and x-ray crystal structure indicated characteristic differences. Based on the findings, we proposed the chromophore-releasing mechanism by a three-state equilibrium, which sufficiently describes both the strong binding and the prompt releasing of the chromophore. We demonstrated that we could bridge the dynamic properties and the static structure features with simple kinetic assumptions to solve the biochemical function.


    Related Citations: 
    • Distributed Computing and NMR Constraint-Based High-Resolution Structure Determination: Applied for Bioactive Peptide Endothelin-1 To Determine C-Terminal Folding.
      Takashima, H.,Mimura, N.,Ohkubo, T.,Yoshida, T.,Tamaoki, H.,Kobayashi, Y.
      (2004) J.Am.Chem.Soc. 126: 4504


    Organizational Affiliation

    Informatics and Knowledge Management at Novartis Institutes for BioMedical Research, Novartis, Ohkubo 8, Tsukuba, Ibaraki 300-2611, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neocarzinostatin
A
113Streptomyces carzinostaticusMutation(s): 0 
Gene Names: ncsA
Find proteins for P0A3R9 (Streptomyces carzinostaticus)
Go to UniProtKB:  P0A3R9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CHR
Query on CHR

Download SDF File 
Download CCD File 
A
NEOCARZINOSTATIN-CHROMOPHORE
NCS-CHROMOPHORE
C35 H33 N O12
QZGIWPZCWHMVQL-UIYAJPBUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CHRKd: 0.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 16000 
  • Conformers Submitted: 60 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 1O5P Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance