1T5M

Structural transitions as determinants of the action of the calcium-dependent antibiotic daptomycin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Transitions as Determinants of the Action of the Calcium-Dependent Antibiotic Daptomycin.

Jung, D.Rozek, A.Okon, M.Hancock, R.E.

(2004) Chem Biol 11: 949

  • DOI: https://doi.org/10.1016/j.chembiol.2004.04.020
  • Primary Citation of Related Structures:  
    1T5M, 1T5N

  • PubMed Abstract: 

    Daptomycin is a cyclic anionic lipopeptide antibiotic recently approved for the treatment of complicated skin infections (Cubicin). Its function is dependent on calcium (as Ca2+). Circular dichroism spectroscopy indicated that daptomycin experienced two structural transitions: a transition upon interaction of daptomycin with Ca2+, and a further transition upon interaction with Ca2+ and the bacterial acidic phospholipid, phosphatidyl glycerol. The Ca2+-dependent insertion of daptomycin into model membranes promoted mild and more pronounced perturbations as assessed by the increase of lipid flip-flop and membrane leakage, respectively. The NMR structure of daptomycin indicated that Ca2+ induced a conformational change in daptomycin that increased its amphipathicity. These results are consistent with the hypothesis that the association of Ca2+ with daptomycin permits it to interact with bacterial membranes with effects that are similar to those of the cationic antimicrobial peptides.


  • Organizational Affiliation

    Department of Microbiology and Immunology, University of British Columbia, 232B-2259 Lower Mall, Vancouver, BC, V6T 1Z4, Canada.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DAPTOMYCIN13Streptomyces filamentosusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DKA
Query on DKA

Download Ideal Coordinates CCD File 
B [auth A]DECANOIC ACID
C10 H20 O2
GHVNFZFCNZKVNT-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
KYN
Query on KYN
A
L-PEPTIDE LINKINGC10 H12 N2 O3TRP
LME
Query on LME
A
L-PEPTIDE LINKINGC6 H11 N O4GLU
ORN
Query on ORN
A
L-PEPTIDE LINKINGC5 H12 N2 O2ALA
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChains NameType/Class2D Diagram3D Interactions
PRD_000217
Query on PRD_000217
A
DaptomycinCyclic lipopeptide / Antibiotic
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-31
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other