This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4o5y

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:57, 20 March 2024) (edit) (undo)
 
(4 intermediate revisions not shown.)
Line 1: Line 1:
 +
==O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine==
==O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine==
-
<StructureSection load='4o5y' size='340' side='right' caption='[[4o5y]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+
<StructureSection load='4o5y' size='340' side='right'caption='[[4o5y]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4o5y]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O5Y FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[4o5y]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O5Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O5Y FirstGlance]. <br>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene><br>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
-
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</scene></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=C6G:6-(CARBOXYMETHOXY)-9-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-9H-PURIN-2-AMINE'>C6G</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4itd|4itd]], [[4ij0|4ij0]], [[4o5w|4o5w]], [[4o5x|4o5x]], [[4o5z|4o5z]]</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=4o5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5y OCA], [https://pdbe.org/4o5y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o5y RCSB], [https://www.ebi.ac.uk/pdbsum/4o5y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o5y ProSAT]</span></td></tr>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4o5y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o5y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o5y RCSB], [http://www.ebi.ac.uk/pdbsum/4o5y PDBsum]</span></td></tr>
+
</table>
-
<table>
+
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
N-Nitrosation of glycine and its derivatives generates potent alkylating agents that can lead to the formation of O(6)-carboxymethylguanine (O(6)-CMG) in DNA. O(6)-CMG has been identified in DNA derived from human colon tissue and its occurrence has been linked to diets high in red and processed meats, implying an association with the induction of colorectal cancer. By analogy to O(6)-methylguanine, O(6)-CMG is expected to be mutagenic, inducing G-to-A mutations that may be the molecular basis of increased cancer risk. Previously, the crystal structure of the DNA dodecamer d(CGCG[O(6)-CMG]ATTCGCG) has been reported, in which O(6)-CMG forms a Watson-Crick-type pair with thymine similar to the canonical A:T pair. In order to further investigate the versatility of O(6)-CMG in base-pair formation, the structure of the DNA dodecamer d(CGC[O(6)-CMG]AATTTGCG) containing O(6)-CMG at a different position has been determined by X-ray crystallography using four crystal forms obtained under conditions containing different solvent ions (Sr(2+), Ba(2+), Mg(2+), K(+) or Na(+)) with and without Hoechst 33258. The most striking finding is that the pairing modes of O(6)-CMG with T are quite different from those previously reported. In the present dodecamer, the T bases are displaced (wobbled) into the major groove to form a hydrogen bond between the thymine N(3) N-H and the carboxyl group of O(6)-CMG. In addition, a water molecule is bridged through two hydrogen bonds between the thymine O(2) atom and the 2-amino group of O(6)-CMG to stabilize the pairing. These interaction modes commonly occur in the four crystal forms, regardless of the differences in crystallization conditions. The previous and the present results show that O(6)-CMG can form a base pair with T in two alternative modes: the Watson-Crick type and a high-wobble type, the nature of which may depend on the DNA-sequence context.
+
-
 
+
-
O(6)-Carboxymethylguanine in DNA forms a sequence context-dependent wobble base-pair structure with thymine.,Zhang F, Tsunoda M, Kikuchi Y, Wilkinson O, Millington CL, Margison GP, Williams DM, Takenaka A Acta Crystallogr D Biol Crystallogr. 2014 Jun;70(Pt 6):1669-79. doi:, 10.1107/S1399004714006178. Epub 2014 May 30. PMID:24914978<ref>PMID:24914978</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Kikuchi, Y.]]
+
[[Category: Large Structures]]
-
[[Category: Margison, G P.]]
+
[[Category: Kikuchi Y]]
-
[[Category: Millington, C L.]]
+
[[Category: Margison GP]]
-
[[Category: Suzuki, K.]]
+
[[Category: Millington CL]]
-
[[Category: Takenaka, A.]]
+
[[Category: Suzuki K]]
-
[[Category: Tsunoda, M.]]
+
[[Category: Takenaka A]]
-
[[Category: Wilkinson, O.]]
+
[[Category: Tsunoda M]]
-
[[Category: Williams, D M.]]
+
[[Category: Wilkinson O]]
-
[[Category: Zhang, F.]]
+
[[Category: Williams DM]]
-
[[Category: Damaged dna]]
+
[[Category: Zhang F]]
-
[[Category: Dna]]
+
-
[[Category: O6-carboxymethylguanine]]
+

Current revision

O6-carboxymethylguanine in DNA forms a sequence context dependent wobble base pair structure with thymine

PDB ID 4o5y

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4o5y"
Personal tools