1g3v
From Proteopedia
(New page: 200px<br /><applet load="1g3v" size="450" color="white" frame="true" align="right" spinBox="true" caption="1g3v, resolution 3.1Å" /> '''CRYSTAL STRUCTURE OF ...) |
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| - | [[Image:1g3v.gif|left|200px]]<br /><applet load="1g3v" size=" | + | [[Image:1g3v.gif|left|200px]]<br /><applet load="1g3v" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1g3v, resolution 3.1Å" /> | caption="1g3v, resolution 3.1Å" /> | ||
'''CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2'''<br /> | '''CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The aim of this study was to clarify whether Ni2+ ions could bind to | + | The aim of this study was to clarify whether Ni2+ ions could bind to guanine bases in a standard B-DNA duplex and eventually induce a B-->Z transition. We have determined by X-ray crystallography at 3.1 A resolution the structure of the alternating deoxynucleotide d(CGTGTACACG), which contains both internal and terminal guanines. The duplex is in the B form. It is shown that nickel ions bind selectively to the N7 atom of guanine 10, which is in an extra-helical position, and guanine 2, which is in the terminal position of the duplex. It does not bind to guanine 4, which lies within a standard B-DNA tract. This simple but unambiguous result proves that nickel ions select between different guanines via steric accessibility. Guanine-Ni2+-guanine bridges among symmetry-related duplexes have also been found. These bridges may explain why Ni2+ ions may act either as a precipitant or a renaturing agent for DNA under certain conditions. The biochemical interaction of nickel with DNA can thus be related to its capacity to specifically bind to B-DNA regions with exposed guanines. Also, from the structural point of view, we have found a terminal cytosine, which forms a C.G:C reverse-Hoogsteen triple structure with a base pair of a neighbor duplex. This type of triplet is seldom found and is here described for the first time for a DNA structure. |
==About this Structure== | ==About this Structure== | ||
| - | 1G3V is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NI as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1G3V is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NI:'>NI</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3V OCA]. |
==Reference== | ==Reference== | ||
Nickel-guanine interactions in DNA: crystal structure of nickel-d[CGTGTACACG]2., Abrescia NA, Huynh-Dinh T, Subirana JA, J Biol Inorg Chem. 2002 Jan;7(1-2):195-9. Epub 2001 Aug 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11862555 11862555] | Nickel-guanine interactions in DNA: crystal structure of nickel-d[CGTGTACACG]2., Abrescia NA, Huynh-Dinh T, Subirana JA, J Biol Inorg Chem. 2002 Jan;7(1-2):195-9. Epub 2001 Aug 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11862555 11862555] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Abrescia, N | + | [[Category: Abrescia, N G.A.]] |
| - | [[Category: Subirana, J | + | [[Category: Subirana, J A.]] |
[[Category: NI]] | [[Category: NI]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: nickel binding]] | [[Category: nickel binding]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:45:46 2008'' |
Revision as of 10:45, 21 February 2008
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CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2
Overview
The aim of this study was to clarify whether Ni2+ ions could bind to guanine bases in a standard B-DNA duplex and eventually induce a B-->Z transition. We have determined by X-ray crystallography at 3.1 A resolution the structure of the alternating deoxynucleotide d(CGTGTACACG), which contains both internal and terminal guanines. The duplex is in the B form. It is shown that nickel ions bind selectively to the N7 atom of guanine 10, which is in an extra-helical position, and guanine 2, which is in the terminal position of the duplex. It does not bind to guanine 4, which lies within a standard B-DNA tract. This simple but unambiguous result proves that nickel ions select between different guanines via steric accessibility. Guanine-Ni2+-guanine bridges among symmetry-related duplexes have also been found. These bridges may explain why Ni2+ ions may act either as a precipitant or a renaturing agent for DNA under certain conditions. The biochemical interaction of nickel with DNA can thus be related to its capacity to specifically bind to B-DNA regions with exposed guanines. Also, from the structural point of view, we have found a terminal cytosine, which forms a C.G:C reverse-Hoogsteen triple structure with a base pair of a neighbor duplex. This type of triplet is seldom found and is here described for the first time for a DNA structure.
About this Structure
1G3V is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Nickel-guanine interactions in DNA: crystal structure of nickel-d[CGTGTACACG]2., Abrescia NA, Huynh-Dinh T, Subirana JA, J Biol Inorg Chem. 2002 Jan;7(1-2):195-9. Epub 2001 Aug 25. PMID:11862555
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