1DAU

Analog of dickerson-drew DNA dodecamer with 6'-alpha-methyl carbocyclic thymidines, NMR, minimized average structure


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: LOWEST ENERGY, BEST AGREEMENT WITH NOE VOLUMES 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The solution conformation of a carbocyclic analog of the Dickerson-Drew dodecamer: comparison with its own X-ray structure and that of the NMR structure of the native counterpart.

Denisov, A.Y.Zamaratski, E.V.Maltseva, T.V.Sandstrom, A.Bekiroglu, S.Altmann, K.H.Egli, M.Chattopadhyaya, J.

(1998) J.Biomol.Struct.Dyn. 16: 547-568

  • DOI: 10.1080/07391102.1998.10508269
  • Primary Citation of Related Structures:  2DAU

  • PubMed Abstract: 
  • The NMR conformation of a carbocyclic analog of the Dickerson-Drew dodecamer [d(CGC-GAAT*T*CGCG)]2 containing 6'-alpha-Me carbocyclic thymidines (T*) has been determined and compared with that of its X-ray structure. The solution structure of the 6'- ...

    The NMR conformation of a carbocyclic analog of the Dickerson-Drew dodecamer [d(CGC-GAAT*T*CGCG)]2 containing 6'-alpha-Me carbocyclic thymidines (T*) has been determined and compared with that of its X-ray structure. The solution structure of the 6'-alpha-Me carbocyclic thymidine modified duplex has also been compared with the solution structure of the corresponding unmodified Dickerson-Drew duplex solved by us under the same experimental conditions. The NMR structures have been based on 24 experimental distance and torsion constraints per residue for [d(CGCGAAT*T*CGCG)]2 (1) and on 21 constraints per residue for the natural counterpart. In general, both final NMR structures are more close to the B-type DNA. The cyclopentane moieties of the carbocyclic thymidine residues adopt C1'-exo B-DNA type puckers (the phase angles P = 136-139 degrees and the puckering amplitudes psi = 36-37 degrees) that are close to their previously published crystal C1'-exo or C2'-endo puckers. The main differences between the two NMR structures are for beta(T*8) and epsilon, xi(T*7) backbone torsions (27-50 degrees ), for basepair twist for the 7-8 and 8-9 basepair steps (5-6 degrees), tilt for the 8-9 step (7 degrees), roll for the 7-8 step (7 degrees), shift for the 7-8 step (0.9A) and slide for the 9-10 step (0.6A). The relatively small deviations of helical structure parameters lead to structural isomorphism of these duplexes in aqueous solutions (atomic RMSD = 1.0A). The difference of the minor groove widths (less than 0.7A) in the core part of the modified duplex in comparison with the native one is much smaller than the difference between the X-ray structures of these duplexes. A detailed comparison of NMR and X-ray structure parameters showed significant monotonic differences (0.9-2.5A) for all basepair slides in both duplexes. Deviations between NMR and X-ray structure parameters for the modified duplex were also found for basepair tilt of the 4-5 step (13 degrees), rolls for the 8-9 and 10-11 steps (16 and 19 degrees), twist of the 3-4 step (8 degrees) and shift of the 9-10 step (0.9A).


    Organizational Affiliation

    Department of Bioorganic Chemistry, Biomedical Center, University of Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*CP*GP*AP*AP*(T32)P*(T32)P*CP*GP*CP*G)-3')A,B12N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
T32
Query on T32
A, B
DNA LINKINGC12 H19 N2 O7 PDT
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 
  • Conformers Submitted: 
  • Selection Criteria: LOWEST ENERGY, BEST AGREEMENT WITH NOE VOLUMES 
Software Package:
Software NamePurpose
AMBERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance