231d
From Proteopedia
(New page: 200px<br /><applet load="231d" size="350" color="white" frame="true" align="right" spinBox="true" caption="231d, resolution 2.400Å" /> '''STRUCTURE OF A DNA-...) |
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==Overview== | ==Overview== | ||
| - | We report the 2.4 A resolution X-ray structure of a complex in which a | + | We report the 2.4 A resolution X-ray structure of a complex in which a small molecule flips a base out of a DNA helical stack. The small molecule is a metalloporphyrin, CuTMPyP4 [copper(II) meso-tetra(N-methyl-4-pyridyl)porphyrin], and the DNA is a hexamer duplex, [d(CGATCG)]2. The porphyrin system, with the copper atom near the helical axis, is located within the helical stack. The porphyrin binds by normal intercalation between the C and G of 5' TCG 3' and by extruding the C of 5' CGA 3'. The DNA forms a distorted right-handed helix with only four normal cross-strand Watson-Crick base pairs. Two pyridyl rings are located in each groove of the DNA. The complex appears to be extensively stabilized by electrostatic interactions between positively charged nitrogen atoms of the pyridyl rings and negatively charged phosphate oxygen atoms of the DNA. Favorable electrostatic interactions appear to draw the porphyrin into the duplex interior, offsetting unfavorable steric clashes between the pyridyl rings and the DNA backbone. These pyridyl-backbone clashes extend the DNA along its axis and preclude formation of van der Waals stacking contacts in the interior of the complex. Stacking contacts are the primary contributor to stability of DNA. The unusual lack of van der Waals stacking contacts in the porphyrin complex destabilizes the DNA duplex and decreases the energetic cost of local melting. Thus extrusion of a base appears to be facilitated by pyridyl-DNA steric clashes. |
==About this Structure== | ==About this Structure== | ||
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Structure of DNA-porphyrin complex., Lipscomb LA, Zhou FX, Presnell SR, Woo RJ, Peek ME, Plaskon RR, Williams LD, Biochemistry. 1996 Mar 5;35(9):2818-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8608116 8608116] | Structure of DNA-porphyrin complex., Lipscomb LA, Zhou FX, Presnell SR, Woo RJ, Peek ME, Plaskon RR, Williams LD, Biochemistry. 1996 Mar 5;35(9):2818-23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8608116 8608116] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Lipscomb, L | + | [[Category: Lipscomb, L A.]] |
| - | [[Category: Peek, M | + | [[Category: Peek, M E.]] |
| - | [[Category: Plaskon, R | + | [[Category: Plaskon, R R.]] |
| - | [[Category: Presnell, S | + | [[Category: Presnell, S R.]] |
| - | [[Category: Williams, L | + | [[Category: Williams, L D.]] |
| - | [[Category: Woo, R | + | [[Category: Woo, R J.]] |
| - | [[Category: Zhou, F | + | [[Category: Zhou, F X.]] |
[[Category: NA]] | [[Category: NA]] | ||
[[Category: PCU]] | [[Category: PCU]] | ||
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[[Category: right handed dna]] | [[Category: right handed dna]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:21:23 2008'' |
Revision as of 14:21, 21 February 2008
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STRUCTURE OF A DNA-PORPHYRIN COMPLEX
Overview
We report the 2.4 A resolution X-ray structure of a complex in which a small molecule flips a base out of a DNA helical stack. The small molecule is a metalloporphyrin, CuTMPyP4 [copper(II) meso-tetra(N-methyl-4-pyridyl)porphyrin], and the DNA is a hexamer duplex, [d(CGATCG)]2. The porphyrin system, with the copper atom near the helical axis, is located within the helical stack. The porphyrin binds by normal intercalation between the C and G of 5' TCG 3' and by extruding the C of 5' CGA 3'. The DNA forms a distorted right-handed helix with only four normal cross-strand Watson-Crick base pairs. Two pyridyl rings are located in each groove of the DNA. The complex appears to be extensively stabilized by electrostatic interactions between positively charged nitrogen atoms of the pyridyl rings and negatively charged phosphate oxygen atoms of the DNA. Favorable electrostatic interactions appear to draw the porphyrin into the duplex interior, offsetting unfavorable steric clashes between the pyridyl rings and the DNA backbone. These pyridyl-backbone clashes extend the DNA along its axis and preclude formation of van der Waals stacking contacts in the interior of the complex. Stacking contacts are the primary contributor to stability of DNA. The unusual lack of van der Waals stacking contacts in the porphyrin complex destabilizes the DNA duplex and decreases the energetic cost of local melting. Thus extrusion of a base appears to be facilitated by pyridyl-DNA steric clashes.
About this Structure
231D is a Protein complex structure of sequences from [1] with and as ligands. Full crystallographic information is available from OCA.
Reference
Structure of DNA-porphyrin complex., Lipscomb LA, Zhou FX, Presnell SR, Woo RJ, Peek ME, Plaskon RR, Williams LD, Biochemistry. 1996 Mar 5;35(9):2818-23. PMID:8608116
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