6RIO

Imidazole Polyamide-DNA complex NMR structure (5'-CGATGTACATCG-3')


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 2000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Sequence-Selective Minor Groove Recognition of a DNA Duplex Containing Synthetic Genetic Components.

Padroni, G.Withers, J.M.Taladriz-Sender, A.Reichenbach, L.F.Parkinson, J.A.Burley, G.A.

(2019) J.Am.Chem.Soc. 141: 9555-9563

  • DOI: 10.1021/jacs.8b12444
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structural basis of minor groove recognition of a DNA duplex containing synthetic genetic information by hairpin pyrrole-imidazole polyamides is described. Hairpin polyamides induce a higher melting stabilization of a DNA duplex containing the un ...

    The structural basis of minor groove recognition of a DNA duplex containing synthetic genetic information by hairpin pyrrole-imidazole polyamides is described. Hairpin polyamides induce a higher melting stabilization of a DNA duplex containing the unnatural P•Z base-pair when an imidazole unit is aligned with a P nucleotide. An NMR structural study showed that the incorporation of two isolated P•Z pairs enlarges the minor groove and slightly narrows the major groove at the site of this synthetic genetic information, relative to a DNA duplex consisting entirely of Watson-Crick base-pairs. Pyrrole-imidazole polyamides bind to a P•Z-containing DNA duplex to form a stability complex, effectively mimick-ing a G•C pair. A structural hallmark of minor groove recognition of a P•Z pair by a polyamide is the reduced level of allosteric distortion induced by binding of a polyamide to a DNA duplex. Understanding the molecular determinants which influence minor groove recognition of DNA containing synthetic genetic components provides the basis to further develop unnatural base-pairs for synthetic biology applications.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-(*(DC5)P*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*(DG3))-3')A,B12Homo
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K4Z
Query on K4Z

Download SDF File 
Download CCD File 
A
3-[3-[[4-[[4-[[4-[[4-[[(2~{R})-2-azaniumyl-4-[[1-methyl-4-[[1-methyl-4-[[1-methyl-4-[(1-methylimidazol-2-yl)carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]pyrrol-2-yl]carbonylamino]butanoyl]amino]-1-methyl-imidazol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]-1-methyl-pyrrol-2-yl]carbonylamino]propanoylamino]propyl-dimethyl-azanium
C58 H74 N22 O10
ZZDDBKPURCHKIT-LDLOPFEMSA-P
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DCZ
Query on DCZ
A, B
DNA OH 5 prime terminusC9 H13 N3 O4

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 2000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Science and Technology Funding CouncilUnited KingdomST/M000125/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/R006857/1
Leverhulme TrustUnited KingdomRPG-2018-149

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references