2M27

Major G-quadruplex structure formed in human VEGF promoter, a monomeric parallel-stranded quadruplex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of the major G-quadruplex formed in the human VEGF promoter in K+: insights into loop interactions of the parallel G-quadruplexes.

Agrawal, P.Hatzakis, E.Guo, K.Carver, M.Yang, D.

(2013) Nucleic Acids Res. 41: 10584-10592

  • DOI: 10.1093/nar/gkt784

  • PubMed Abstract: 
  • Vascular endothelial growth factor (VEGF) proximal promoter region contains a poly G/C-rich element that is essential for basal and inducible VEGF expression. The guanine-rich strand on this tract has been shown to form the DNA G-quadruplex structure ...

    Vascular endothelial growth factor (VEGF) proximal promoter region contains a poly G/C-rich element that is essential for basal and inducible VEGF expression. The guanine-rich strand on this tract has been shown to form the DNA G-quadruplex structure, whose stabilization by small molecules can suppress VEGF expression. We report here the nuclear magnetic resonance structure of the major intramolecular G-quadruplex formed in this region in K(+) solution using the 22mer VEGF promoter sequence with G-to-T mutations of two loop residues. Our results have unambiguously demonstrated that the major G-quadruplex formed in the VEGF promoter in K(+) solution is a parallel-stranded structure with a 1:4:1 loop-size arrangement. A unique capping structure was shown to form in this 1:4:1 G-quadruplex. Parallel-stranded G-quadruplexes are commonly found in the human promoter sequences. The nuclear magnetic resonance structure of the major VEGF G-quadruplex shows that the 4-nt middle loop plays a central role for the specific capping structures and in stabilizing the most favored folding pattern. It is thus suggested that each parallel G-quadruplex likely adopts unique capping and loop structures by the specific middle loops and flanking segments, which together determine the overall structure and specific recognition sites of small molecules or proteins.


    Organizational Affiliation

    Department of Pharmacology and Toxiocology, College of Pharmacy, University of Arizona, 1703 E. Mabel St, Tucson, AZ 85721, USA, Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA and The Arizona Cancer Center, Tucson, AZ 85724, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA_(5'-D(*CP*GP*GP*GP*GP*CP*GP*GP*GP*CP*CP*TP*TP*GP*GP*GP*CP*GP*GP*GP*GP*T)-3')_A22Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2014-09-17
    Type: Other, Structure summary