Summary information and primary citation

PDB-id
5zev
Class
DNA
Method
NMR
Summary
Solution structure of g-quadruplex formed in vegfr-2 proximal promoter sequence
Reference
Liu Y, Lan W, Wang C, Cao C (2018): "A putative G-quadruplex structure in the proximal promoter ofVEGFR-2has implications for drug design to inhibit tumor angiogenesis." J. Biol. Chem., 293, 8947-8955. doi: 10.1074/jbc.RA118.002666.
Abstract
Tumor angiogenesis is mainly regulated by vascular endothelial growth factor (VEGF) produced by cancer cells. It is active on the endothelium via VEGF receptor 2 (VEGFR-2). G-quadruplexes are DNA secondary structures formed by guanine-rich sequences, for example, within gene promoters where they may contribute to transcriptional activity. The proximal promoter of <i>VEGFR-2</i> contains a G-quadruplex, which has been suggested to interact with small molecules that inhibit <i>VEGFR-2</i> expression and thereby tumor angiogenesis. However, its structure is not known. Here, we determined its NMR solution structure, which is composed of three stacked G-tetrads containing three <i>syn</i> guanines. The first guanine (G<sub>1</sub>) is positioned within the central G-tetrad. We also observed that a noncanonical, V-shaped loop spans three G-tetrad planes, including no bridging nucleotides. A long and diagonal loop, which includes six nucleotides, connects reversal double chains. With a melting temperature of 54.51 °C, the scaffold of this quadruplex is stabilized by one G-tetrad plane stacking with one nonstandard bp, G<sub>3</sub>-C<sub>8</sub>, whose bases interact with each other through only one hydrogen bond. In summary, the NMR solution structure of the G-quadruplex in the proximal promoter region of the <i>VEGFR-2</i> gene reported here has uncovered its key features as a potential anticancer drug target.
G4 notes
3 G-tetrads, 1 G4 helix, 1 G4 stem, UDDD, hybrid4, 1+3, 2(D+PX)

Cartoon-block schematics in six views (download the tarball)

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List of 3 G-tetrads

 1 glyco-bond=s--- sugar=-.3. groove=w--n planarity=0.196 type=other  Z- nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG22
 2 glyco-bond=--ss sugar=3.-3 groove=-w-n planarity=0.203 type=other  Z+ nts=4 GGGG A.DG2,A.DG13,A.DG9,A.DG21
 3 glyco-bond=--s- sugar=-33- groove=-wn- planarity=0.185 type=other  O+ nts=4 GGGG A.DG11,A.DG16,A.DG20,A.DG23

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 3 G-tetrads, INTRA-molecular, with 1 stem
 1  glyco-bond=--ss sugar=3.-3 groove=-w-n WC-->Major Z+ nts=4 GGGG A.DG2,A.DG13,A.DG9,A.DG21
 2  glyco-bond=s--- sugar=-.3. groove=w--n Major-->WC Z- nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG22
 3  glyco-bond=s--- sugar=33-- groove=w--n Major-->WC O+ nts=4 GGGG A.DG20,A.DG16,A.DG11,A.DG23
  step#1  mm(<>,outward)  area=8.81  rise=2.84 twist=31.5
  step#2  pm(>>,forward)  area=12.04 rise=3.40 twist=31.7
  strand#1 DNA glyco-bond=-ss sugar=3-3 nts=3 GGG A.DG2,A.DG1,A.DG20
  strand#2 DNA glyco-bond=--- sugar=..3 nts=3 GGG A.DG13,A.DG15,A.DG16
  strand#3 DNA glyco-bond=s-- sugar=-3- nts=3 GGG A.DG9,A.DG10,A.DG11
  strand#4 DNA glyco-bond=s-- sugar=3.- nts=3 GGG A.DG21,A.DG22,A.DG23

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2 stacking diagrams 
 1  glyco-bond=--ss sugar=3.-3 groove=-w-n WC-->Major Z+ nts=4 GGGG A.DG2,A.DG13,A.DG9,A.DG21
 2  glyco-bond=s--- sugar=-.3. groove=w--n Major-->WC Z- nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG22
  step#1  mm(<>,outward)  area=8.81  rise=2.84 twist=31.5

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 2  glyco-bond=s--- sugar=-.3. groove=w--n Major-->WC Z- nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG22
 3  glyco-bond=s--- sugar=33-- groove=w--n Major-->WC O+ nts=4 GGGG A.DG20,A.DG16,A.DG11,A.DG23
  step#2  pm(>>,forward)  area=12.04 rise=3.40 twist=31.7

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List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 2 G-tetrads, 3 loops, INTRA-molecular, UDDD, hybrid4, 1+3, 2(D+PX)
 1  glyco-bond=s--- sugar=-.3. groove=w--n Major-->WC Z- nts=4 GGGG A.DG1,A.DG15,A.DG10,A.DG22
 2  glyco-bond=--ss sugar=3.-3 groove=-w-n WC-->Major Z+ nts=4 GGGG A.DG2,A.DG13,A.DG9,A.DG21
  step#1  mm(<>,outward)  area=8.81  rise=2.84 twist=31.5
  strand#1  U DNA glyco-bond=s- sugar=-3 nts=2 GG A.DG1,A.DG2
  strand#2* D DNA glyco-bond=-- sugar=.. nts=2 GG A.DG15,A.DG13 bulged-nts=1 A A.DA14
  strand#3  D DNA glyco-bond=-s sugar=3- nts=2 GG A.DG10,A.DG9
  strand#4  D DNA glyco-bond=-s sugar=.3 nts=2 GG A.DG22,A.DG21
  loop#1 type=diagonal  strands=[#1,#3] nts=6 GTACCC A.DG3,A.DT4,A.DA5,A.DC6,A.DC7,A.DC8
  loop#2 type=propeller strands=[#3,#2] nts=2 GT A.DG11,A.DT12
  loop#3 type=diag-prop strands=[#2,#4] nts=5 GTGCG A.DG16,A.DT17,A.DG18,A.DC19,A.DG20

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List of 2 non-stem G4-loops (including the two closing Gs)

 1 type=lateral   helix=#1 nts=5 GTGCG A.DG16,A.DT17,A.DG18,A.DC19,A.DG20
 2 type=V-shaped  helix=#1 nts=4 GGGG A.DG20,A.DG21,A.DG22,A.DG23