1KLL

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

• PDB DOI: https://doi.org/10.2210/pdb1KLL/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Streptomyces lavendulae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-12-12 Released: 2002-07-19 
• Deposition Author(s): Martin, T.W., Dauter, Z., Devedjiev, Y., Sheffield, P., Jelen, F., He, M., Sherman, D., Otlewski, J., Derewenda, Z.S., Derewenda, U.

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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 

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

• PubMed: 12121648 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 14.89 kDa 
• Atom Count: 1,176 
• Modelled Residue Count: 128 
• Deposited Residue Count: 130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
mitomycin-binding protein	A	130	Streptomyces lavendulae	Mutation(s): 2
UniProt
Find proteins for O05205 (Streptomyces lavendulae) Explore O05205  Go to UniProtKB:  O05205

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MC	B [auth A]	1,2-CIS-1-HYDROXY-2,7-DIAMINO-MITOSENE C14 H16 N4 O5 XNHZZRIKMUCTHU-QTTZVWFDSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

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 = 44.751	α = 90
b = 60.458	β = 106.78
c = 44.077	γ = 90

Software Package:

Software Name	Purpose
SHELXS	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-07-19 
Deposition Author(s): Martin, T.W., Dauter, Z., Devedjiev, Y., Sheffield, P., Jelen, F., He, M., Sherman, D., Otlewski, J., Derewenda, Z.S., Derewenda, U.

Revision History  

• 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