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| | ==X-ray structure of 7-deaza-dG and Z3dU modified duplex CGCGAATXCZCG== | | ==X-ray structure of 7-deaza-dG and Z3dU modified duplex CGCGAATXCZCG== |
| - | <StructureSection load='2qef' size='340' side='right' caption='[[2qef]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='2qef' size='340' side='right'caption='[[2qef]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2qef]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QEF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QEF FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2qef]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QEF FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=7GU:7-DEAZA-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>7GU</scene>, <scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2qeg|2qeg]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7GU:7-DEAZA-2-DEOXYGUANOSINE-5-MONOPHOSPHATE'>7GU</scene>, <scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2-DEOXYURIDINE-5-MONOPHOSPHATE'>ZDU</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2qef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qef OCA], [http://pdbe.org/2qef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qef RCSB], [http://www.ebi.ac.uk/pdbsum/2qef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qef ProSAT]</span></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=2qef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qef OCA], [https://pdbe.org/2qef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qef RCSB], [https://www.ebi.ac.uk/pdbsum/2qef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qef ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Egli, M]] | + | [[Category: Large Structures]] |
| - | [[Category: Ganguly, M]] | + | [[Category: Egli M]] |
| - | [[Category: Gold, B]] | + | [[Category: Ganguly M]] |
| - | [[Category: Li, F]] | + | [[Category: Gold B]] |
| - | [[Category: Marky, L A]] | + | [[Category: Li F]] |
| - | [[Category: Stone, M P]] | + | [[Category: Marky LA]] |
| - | [[Category: Wang, F]] | + | [[Category: Stone MP]] |
| - | [[Category: 7-deaza-dg]]
| + | [[Category: Wang F]] |
| - | [[Category: B-dna]]
| + | |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Z3du]]
| + | |
| Structural highlights
Publication Abstract from PubMed
Site-specific insertion of 5-(3-aminopropyl)-2'-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7)T (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19)T (20)C (21) Z (22)C (23)G (24))-3' (named DDD (Z10)) and 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7) X (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19) X (20)C (21) Z (22)C (23)G (24))-3' (named DDD (2+Z10)) (X = Z3dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD (2+Z10) duplex reveals that the tethered cations at base pairs A (5).X (20) and X (8).A (17) extend within the major groove in the 3'-direction, toward conserved Mg (2+) binding sites located adjacent to N+2 base pairs C (3).Z (22) and Z (10).C (15). Bridging waters located between the tethered amines and either Z (10) or Z (22) O (6) stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD (2+Z10) duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z (10) O (6) and Z (22) O (6). The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C.G base pair, facilitating interstrand cross-linking.
A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards.,Wang F, Li F, Ganguly M, Marky LA, Gold B, Egli M, Stone MP Biochemistry. 2008 Jul 8;47(27):7147-57. Epub 2008 Jun 13. PMID:18549246[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Wang F, Li F, Ganguly M, Marky LA, Gold B, Egli M, Stone MP. A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards. Biochemistry. 2008 Jul 8;47(27):7147-57. Epub 2008 Jun 13. PMID:18549246 doi:http://dx.doi.org/10.1021/bi800375m
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