6xt7

From Proteopedia

(Difference between revisions)

Revision as of 09:12, 28 December 2022

Tel25 Hybrid Four-quartet G-quadruplex with K+

Structural highlights

6xt7 is a 4 chain structure with sequence from Tetrahymena thermophila. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized G-tetrads. GQs play an important role in a variety of biological processes and may form at telomeres and oncogene promoters among other genomic locations. Here, we investigate nine variants of telomeric DNA from Tetrahymena thermophila with the repeat (TTGGGG)n. Biophysical data indicate that the sequences fold into stable four-tetrad GQs which adopt multiple conformations according to native PAGE. Excitingly, we solved the crystal structure of two variants, TET25 and TET26. The two variants differ by the presence of a 3'-T yet adopt different GQ conformations. TET25 forms a hybrid [3 + 1] GQ and exhibits a rare 5'-top snapback feature. Consequently, TET25 contains four loops: three lateral (TT, TT, and GTT) and one propeller (TT). TET26 folds into a parallel GQ with three TT propeller loops. To the best of our knowledge, TET25 and TET26 are the first reported hybrid and parallel four-tetrad unimolecular GQ structures. The results presented here expand the repertoire of available GQ structures and provide insight into the intricacy and plasticity of the 3D architecture adopted by telomeric repeats from T. thermophila and GQs in general.

The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes.,Beseiso D, Chen EV, McCarthy SE, Martin KN, Gallagher EP, Miao J, Yatsunyk LA Nucleic Acids Res. 2022 Mar 21;50(5):2959-2972. doi: 10.1093/nar/gkac091. PMID:35212369^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Beseiso D, Chen EV, McCarthy SE, Martin KN, Gallagher EP, Miao J, Yatsunyk LA. The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes. Nucleic Acids Res. 2022 Mar 21;50(5):2959-2972. doi: 10.1093/nar/gkac091. PMID:35212369 doi:http://dx.doi.org/10.1093/nar/gkac091

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6xt7"

Categories: Large Structures | Tetrahymena thermophila | McCarthy SE | Yatsunyk LA

@@ Line 3: / Line 3: @@
 <StructureSection load='6xt7' size='340' side='right'caption='[[6xt7]], [[Resolution|resolution]] 1.56&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6xt7]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XT7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XT7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6xt7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Tetrahymena_thermophila Tetrahymena thermophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XT7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XT7 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6xt7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xt7 OCA], [https://pdbe.org/6xt7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xt7 RCSB], [https://www.ebi.ac.uk/pdbsum/6xt7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xt7 ProSAT]</span></td></tr>
@@ Line 9: / Line 9: @@
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
-Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. We report here on an analysis of the hydration arrangements around selected folded quadruplex DNAs, which has revealed several prominent features that re-occur in related structures. Many of the primary-sphere water molecules are found in the grooves and loop regions of these structures. At least one groove in anti-parallel and hybrid quadruplex structures is long and narrow and contains an extensive spine of linked primary-sphere water molecules. This spine is analogous to but fundamentally distinct from the well-characterized spine observed in the minor groove of A/T-rich duplex DNA, in that every water molecule in the continuous quadruplex spines makes a direct hydrogen bond contact with groove atoms, principally phosphate oxygen atoms lining groove walls and guanine base nitrogen atoms on the groove floor. By contrast, parallel quadruplexes do not have extended grooves, but primary-sphere water molecules still cluster in them and are especially associated with the loops, helping to stabilize loop conformations.
+G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized G-tetrads. GQs play an important role in a variety of biological processes and may form at telomeres and oncogene promoters among other genomic locations. Here, we investigate nine variants of telomeric DNA from Tetrahymena thermophila with the repeat (TTGGGG)n. Biophysical data indicate that the sequences fold into stable four-tetrad GQs which adopt multiple conformations according to native PAGE. Excitingly, we solved the crystal structure of two variants, TET25 and TET26. The two variants differ by the presence of a 3'-T yet adopt different GQ conformations. TET25 forms a hybrid [3 + 1] GQ and exhibits a rare 5'-top snapback feature. Consequently, TET25 contains four loops: three lateral (TT, TT, and GTT) and one propeller (TT). TET26 folds into a parallel GQ with three TT propeller loops. To the best of our knowledge, TET25 and TET26 are the first reported hybrid and parallel four-tetrad unimolecular GQ structures. The results presented here expand the repertoire of available GQ structures and provide insight into the intricacy and plasticity of the 3D architecture adopted by telomeric repeats from T. thermophila and GQs in general.
-Water spines and networks in G-quadruplex structures.,Li K, Yatsunyk L, Neidle S Nucleic Acids Res. 2020 Dec 8. pii: 6027822. doi: 10.1093/nar/gkaa1177. PMID:33290519<ref>PMID:33290519</ref>
+The first crystal structures of hybrid and parallel four-tetrad intramolecular G-quadruplexes.,Beseiso D, Chen EV, McCarthy SE, Martin KN, Gallagher EP, Miao J, Yatsunyk LA Nucleic Acids Res. 2022 Mar 21;50(5):2959-2972. doi: 10.1093/nar/gkac091. PMID:35212369<ref>PMID:35212369</ref>
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
@@ Line 21: / Line 21: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: McCarthy, S E]]
+[[Category: Tetrahymena thermophila]]
-[[Category: Yatsunyk, L A]]
+[[Category: McCarthy SE]]
-[[Category: Dna]]
+[[Category: Yatsunyk LA]]
-[[Category: Four-quartet]]
-[[Category: G-quadruplex]]
-[[Category: Hybrid]]
-[[Category: Lateral loop]]
-[[Category: Propeller loop]]

6xt7

From Proteopedia

Revision as of 09:12, 28 December 2022

Tel25 Hybrid Four-quartet G-quadruplex with K+

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox