1KLL

Molecular basis of mitomycin C resictance in streptomyces: Crystal structures of the MRD protein with and without a drug derivative


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.124 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Molecular basis of mitomycin C resistance in streptomyces: structure and function of the MRD protein.

Martin, T.W.Dauter, Z.Devedjiev, Y.Sheffield, P.Jelen, F.He, M.Sherman, D.H.Otlewski, J.Derewenda, Z.S.Derewenda, U.

(2002) Structure 10: 933-942

  • DOI: https://doi.org/10.1016/s0969-2126(02)00778-5
  • Primary Citation of Related Structures:  
    1KLL, 1KMZ

  • PubMed Abstract: 

    Mitomycin C (MC) is a potent anticancer agent. Streptomyces lavendulae, which produces MC, protects itself from the lethal effects of the drug by expressing several resistance proteins. One of them (MRD) binds MC and functions as a drug exporter. We report the crystal structure of MRD and its complex with an MC metabolite, 1,2-cis-1-hydroxy-2,7-diaminomitosene, at 1.5 A resolution. The drug is sandwiched by pi-stacking interactions of His-38 and Trp-108. MRD is a dimer. The betaalphabetabetabeta fold of the MRD molecule is reminiscent of methylmalonyl-CoA epimerase, bleomycin resistance proteins, glyoxalase I, and extradiol dioxygenases. The location of the binding site is identical to the ones in evolutionarily related enzymes, suggesting that the protein may have been recruited from a different metabolic pathway.


  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Health Sciences System, Charlottesville 22908, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mitomycin-binding protein130Streptomyces lavendulaeMutation(s): 2 
UniProt
Find proteins for O05205 (Streptomyces lavendulae)
Explore O05205 
Go to UniProtKB:  O05205
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05205
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MC
Query on MC

Download Ideal Coordinates CCD File 
B [auth A]1,2-CIS-1-HYDROXY-2,7-DIAMINO-MITOSENE
C14 H16 N4 O5
XNHZZRIKMUCTHU-QTTZVWFDSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.124 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.751α = 90
b = 60.458β = 106.78
c = 44.077γ = 90
Software Package:
Software NamePurpose
SHELXSphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-11-20
    Changes: Data collection, Structure summary