1O5P

Solution Structure of holo-Neocarzinostatin

PDB DOI: https://doi.org/10.2210/pdb1O5P/pdb
BMRB: 5969

Classification: ANTIBIOTIC
Organism(s): Streptomyces carzinostaticus
Mutation(s): No

Deposited: 2003-10-04 Released: 2003-10-14
Deposition Author(s): Takashima, H., Ishino, T., Yoshida, T., Hasuda, K., Ohkubo, T., Kobayashi, Y.

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 1.4 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

PubMed: 15640161 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M411579200
Primary Citation of Related Structures:
1O5P

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 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 11.76 kDa
Atom Count: 826
Modelled Residue Count: 113
Deposited Residue Count: 113
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neocarzinostatin	A	113	Streptomyces carzinostaticus	Mutation(s): 0
UniProt
Find proteins for P0A3R9 (Streptomyces carzinostaticus) Explore P0A3R9 Go to UniProtKB: P0A3R9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A3R9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CHR Query on CHR Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NEOCARZINOSTATIN-CHROMOPHORE C₃₅ H₃₃ N O₁₂ QZGIWPZCWHMVQL-UIYAJPBUSA-N		Interactions Focus chain B [auth A]