Detailed DSSR results for the G-quadruplex: PDB entry 2lxq
Created and maintained by Xiang-Jun Lu <xiangjun@x3dna.org>
Citation: Please cite the NAR'20 DSSR-PyMOL schematics paper and/or the NAR'15 DSSR method paper.
Summary information
- PDB id
- 2lxq
- Class
- DNA
- Method
- NMR
- Summary
- Monomeric pile g-quadruplex DNA from neisseria gonorrhoeae
- Reference
- Kuryavyi V, Cahoon LA, Seifert HS, Patel DJ (2012): "RecA-Binding pilE G4 Sequence Essential for Pilin Antigenic Variation Forms Monomeric and 5' End-Stacked Dimeric Parallel G-Quadruplexes." Structure, 20, 2090-2102. doi: 10.1016/j.str.2012.09.013.
- Abstract
- Neisseria gonorrhoeae is an obligate human pathogen that can escape immune surveillance through antigenic variation of surface structures such as pili. A G-quadruplex-forming (G4) sequence (5'-G(3)TG(3)TTG(3)TG(3)) located upstream of the N. gonorrhoeae pilin expression locus (pilE) is necessary for initiation of pilin antigenic variation, a recombination-based, high-frequency, diversity-generation system. We have determined NMR-based structures of the all parallel-stranded monomeric and 5' end-stacked dimeric pilE G-quadruplexes in monovalent cation-containing solutions. We demonstrate that the three-layered all parallel-stranded monomeric pilE G-quadruplex containing single-residue double-chain reversal loops, which can be modeled without steric clashes into the 3 nt DNA-binding site of RecA, binds and promotes E. coli RecA-mediated strand exchange in vitro. We discuss how interactions between RecA and monomeric pilE G-quadruplex could facilitate the specialized recombination reactions leading to pilin diversification.
- G4 notes
- 3 G-tetrads, 1 G4 helix, 1 G4 stem, 3(-P-P-P), parallel(4+0), UUUU
Base-block schematics in six views
List of 3 G-tetrads
1 glyco-bond=---- sugar=---- groove=---- planarity=0.120 type=planar nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG16 2 glyco-bond=---- sugar=-.-- groove=---- planarity=0.081 type=planar nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 3 glyco-bond=---- sugar=---- groove=---- planarity=0.198 type=other nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
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-tetrad layers, INTRA-molecular, with 1 stem
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG16 2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 step#1 pm(>>,forward) area=11.70 rise=3.47 twist=29.0 step#2 pm(>>,forward) area=13.75 rise=3.56 twist=24.8 strand#1 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG12,A.DG13,A.DG14 strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG16,A.DG17,A.DG18 |
| 2 stacking diagrams | |
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG16 |
 |
2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 |
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, 3 G-tetrad layers, 3 loops, INTRA-molecular, UUUU, parallel, 3(-P-P-P), parallel(4+0)
 |
1 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG3,A.DG7,A.DG12,A.DG16 2 glyco-bond=---- sugar=-.-- groove=---- WC-->Major nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17 3 glyco-bond=---- sugar=---- groove=---- WC-->Major nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18 step#1 pm(>>,forward) area=11.70 rise=3.47 twist=29.0 step#2 pm(>>,forward) area=13.75 rise=3.56 twist=24.8 strand#1 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG3,A.DG4,A.DG5 strand#2 U DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG7,A.DG8,A.DG9 strand#3 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG12,A.DG13,A.DG14 strand#4 U DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG16,A.DG17,A.DG18 loop#1 type=propeller strands=[#1,#2] nts=1 T A.DT6 loop#2 type=propeller strands=[#2,#3] nts=2 TT A.DT10,A.DT11 loop#3 type=propeller strands=[#3,#4] nts=1 T A.DT15 |