1djd: Difference between revisions

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-[[Image:1djd.gif|left|200px]]<br /><applet load="1djd" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1djd" />
-'''THE SOLUTION STRUCTURE OF A NON-BAY REGION 11R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE'''<br />
-==Overview==
+==THE SOLUTION STRUCTURE OF A NON-BAY REGION 11R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE==
-The structure of the non-bay region (8S,9R,10S,11R)-N(6)-[11-(8,9,10, 11-tetrahydro-8,9,10-trihydroxybenz[a]anthracenyl)]-2'-de oxyadenosyl, adduct at X(6) of 5'-d(CGGACXAGAAG)-3'.5'-d(CTTCTTGTCCG)-3', incorporating, codons 60, 61 (underlined), and 62 of the human N-ras protooncogene, was, determined. Molecular dynamics simulations were restrained by 475 NOEs, from (1)H NMR. The benz[a]anthracene moiety intercalated above the 5'-face, of the modified base pair and from the major groove. The duplex suffered, distortion at and immediately adjacent to the adduct site. This was, evidenced by the disruption of the Watson-Crick base pairing for X(6) x, T(17) and A(7) x T(16) and the increased rise of 7.7 A between base pairs, C(5) x G(18) and X(6) x T(17). Increased disorder was observed as excess, line width of proton resonances near the lesion site. Comparison with the, bay region benzo[a]pyrene [Zegar, I. S., Kim, S. J., Johansen, T. N., Horton, P. J., Harris, C. M., Harris, T. M., and Stone, M. P. (1996), Biochemistry 35, 6212-6224] and bay region benz[a]anthracene [Li, Z., Mao, H., Kim, H.-Y., Tamura, P. J., Harris, C. M., Harris, T. M., and Stone, M., P. (1999) Biochemistry 38, 2969-2981] adducts with the corresponding, stereochemistry and at the same site shows that this non-bay region, benz[a]anthracene lesion assumes different base pair geometry, in addition, to exhibiting greater disorder. These differences are attributed to the, loss of the bay region ring. The results suggest the bay region ring, contributes to base stacking interactions at the lesion site. These, structural differences between the non-bay and bay region lesions are, correlated with site-specific mutagenesis data. The bay region, benzo[a]pyrene and bay region benz[a]anthracene adducts were poorly, replicated in vivo, and induced A --&gt; G mutations. In contrast, the, non-bay region benz[a]anthracene adduct was easily bypassed in vivo and, was nonmutagenic.
+<StructureSection load='1djd' size='340' side='right'caption='[[1djd]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1djd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DJD FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TBT:8,9,10,11-TETRAHYDRO-BENZO[A]ANTHRACENE-8,9,10-TRIOL'>TBT</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=1djd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1djd OCA], [https://pdbe.org/1djd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1djd RCSB], [https://www.ebi.ac.uk/pdbsum/1djd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1djd ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of the non-bay region (8S,9R,10S,11R)-N(6)-[11-(8,9,10, 11-tetrahydro-8,9,10-trihydroxybenz[a]anthracenyl)]-2'-de oxyadenosyl adduct at X(6) of 5'-d(CGGACXAGAAG)-3'.5'-d(CTTCTTGTCCG)-3', incorporating codons 60, 61 (underlined), and 62 of the human N-ras protooncogene, was determined. Molecular dynamics simulations were restrained by 475 NOEs from (1)H NMR. The benz[a]anthracene moiety intercalated above the 5'-face of the modified base pair and from the major groove. The duplex suffered distortion at and immediately adjacent to the adduct site. This was evidenced by the disruption of the Watson-Crick base pairing for X(6) x T(17) and A(7) x T(16) and the increased rise of 7.7 A between base pairs C(5) x G(18) and X(6) x T(17). Increased disorder was observed as excess line width of proton resonances near the lesion site. Comparison with the bay region benzo[a]pyrene [Zegar, I. S., Kim, S. J., Johansen, T. N., Horton, P. J., Harris, C. M., Harris, T. M., and Stone, M. P. (1996) Biochemistry 35, 6212-6224] and bay region benz[a]anthracene [Li, Z., Mao, H., Kim, H.-Y., Tamura, P. J., Harris, C. M., Harris, T. M., and Stone, M. P. (1999) Biochemistry 38, 2969-2981] adducts with the corresponding stereochemistry and at the same site shows that this non-bay region benz[a]anthracene lesion assumes different base pair geometry, in addition to exhibiting greater disorder. These differences are attributed to the loss of the bay region ring. The results suggest the bay region ring contributes to base stacking interactions at the lesion site. These structural differences between the non-bay and bay region lesions are correlated with site-specific mutagenesis data. The bay region benzo[a]pyrene and bay region benz[a]anthracene adducts were poorly replicated in vivo, and induced A --&gt; G mutations. In contrast, the non-bay region benz[a]anthracene adduct was easily bypassed in vivo and was nonmutagenic.
-==About this Structure==
+Role of a polycyclic aromatic hydrocarbon bay region ring in modulating DNA adduct structure: the non-bay region (8S,9R,10S, 11R)-N(6)-[11-(8,9,10,11-tetrahydro-8,9, 10-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct in codon 61 of the human N-ras protooncogene.,Li Z, Kim HY, Tamura PJ, Harris CM, Harris TM, Stone MP Biochemistry. 1999 Nov 9;38(45):14820-32. PMID:10555964<ref>PMID:10555964</ref>
-DJD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with TBT as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DJD OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Role of a polycyclic aromatic hydrocarbon bay region ring in modulating DNA adduct structure: the non-bay region (8S,9R,10S, 11R)-N(6)-[11-(8,9,10,11-tetrahydro-8,9, 10-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct in codon 61 of the human N-ras protooncogene., Li Z, Kim HY, Tamura PJ, Harris CM, Harris TM, Stone MP, Biochemistry. 1999 Nov 9;38(45):14820-32. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10555964 10555964]
+</div>
-[[Category: Protein complex]]
+<div class="pdbe-citations 1djd" style="background-color:#fffaf0;"></div>
-[[Category: Harris, C.M.]]
+== References ==
-[[Category: Harris, T.M.]]
+<references/>
-[[Category: Kim, H.Y.]]
+__TOC__
-[[Category: Li, Z.]]
+</StructureSection>
-[[Category: Stone, M.P.]]
+[[Category: Homo sapiens]]
-[[Category: Tamura, P.J.]]
+[[Category: Large Structures]]
-[[Category: TBT]]
+[[Category: Harris CM]]
-[[Category: benz[a]anthracene-dna duplex]]
+[[Category: Harris TM]]
+[[Category: Kim HY]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:11:43 2007''
+[[Category: Li Z]]
+[[Category: Stone MP]]
+[[Category: Tamura PJ]]