1nlc

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 4: Line 4:
==Overview==
==Overview==
-
Metal ions, and magnesium in particular, are known to be involved in RNA, folding by stabilizing secondary and tertiary structures, and, as, cofactors, in RNA enzymatic activity. We have conducted a systematic, crystallographic analysis of cation binding to the duplex form of the, HIV-1 RNA dimerization initiation site for the subtype-A and -B natural, sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+, Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)6]3+ and [Ru (NH3)6]3+, were found to bind to the DIS duplex structure. Although the two sequences, are very similar, strong differences were found in their cation binding, properties. Divalent cations bind almost exclusively, as Mg2+, at, 'Hoogsteen' sites of guanine residues, with a cation-dependent affinity, for each site. Notably, a given cation can have very different affinities, for a priori equivalent sites within the same molecule. Surprisingly, none, of the two hexammines used were able to efficiently replace hexahydrated, magnesium. Instead, [Co (NH3)4]3+ was seen bound by inner-sphere, coordination to the RNA. This raises some questions about the practical, use of [Co (NH3)6]3+ as a [Mg (H2O)6]2+ mimetic. Also very unexpected was, the binding of the small Au3+ cation exactly between the Watson-Crick, sites of a G-C base pair after an obligatory deprotonation of N1 of the, guanine base. This extensive study of metal ion binding using X-ray, crystallography significantly enriches our knowledge on the binding of, middleweight or heavy metal ions to RNA, particularly compared with, magnesium.
+
Metal ions, and magnesium in particular, are known to be involved in RNA folding by stabilizing secondary and tertiary structures, and, as cofactors, in RNA enzymatic activity. We have conducted a systematic crystallographic analysis of cation binding to the duplex form of the HIV-1 RNA dimerization initiation site for the subtype-A and -B natural sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+, Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)6]3+ and [Ru (NH3)6]3+ were found to bind to the DIS duplex structure. Although the two sequences are very similar, strong differences were found in their cation binding properties. Divalent cations bind almost exclusively, as Mg2+, at 'Hoogsteen' sites of guanine residues, with a cation-dependent affinity for each site. Notably, a given cation can have very different affinities for a priori equivalent sites within the same molecule. Surprisingly, none of the two hexammines used were able to efficiently replace hexahydrated magnesium. Instead, [Co (NH3)4]3+ was seen bound by inner-sphere coordination to the RNA. This raises some questions about the practical use of [Co (NH3)6]3+ as a [Mg (H2O)6]2+ mimetic. Also very unexpected was the binding of the small Au3+ cation exactly between the Watson-Crick sites of a G-C base pair after an obligatory deprotonation of N1 of the guanine base. This extensive study of metal ion binding using X-ray crystallography significantly enriches our knowledge on the binding of middleweight or heavy metal ions to RNA, particularly compared with magnesium.
==About this Structure==
==About this Structure==
Line 20: Line 20:
[[Category: zinc]]
[[Category: zinc]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 16:29:24 2008''
+
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:07:23 2008''

Revision as of 12:07, 21 February 2008

Image:1nlc.jpg

1nlc, resolution 1.85Å

Drag the structure with the mouse to rotate

HIV-1 DIS(Mal) duplex Zn-soaked

Overview

Metal ions, and magnesium in particular, are known to be involved in RNA folding by stabilizing secondary and tertiary structures, and, as cofactors, in RNA enzymatic activity. We have conducted a systematic crystallographic analysis of cation binding to the duplex form of the HIV-1 RNA dimerization initiation site for the subtype-A and -B natural sequences. Eleven ions (K+, Pb2+, Mn2+, Ba2+, Ca2+, Cd2+, Sr2+, Zn2+, Co2+, Au3+ and Pt4+) and two hexammines [Co (NH3)6]3+ and [Ru (NH3)6]3+ were found to bind to the DIS duplex structure. Although the two sequences are very similar, strong differences were found in their cation binding properties. Divalent cations bind almost exclusively, as Mg2+, at 'Hoogsteen' sites of guanine residues, with a cation-dependent affinity for each site. Notably, a given cation can have very different affinities for a priori equivalent sites within the same molecule. Surprisingly, none of the two hexammines used were able to efficiently replace hexahydrated magnesium. Instead, [Co (NH3)4]3+ was seen bound by inner-sphere coordination to the RNA. This raises some questions about the practical use of [Co (NH3)6]3+ as a [Mg (H2O)6]2+ mimetic. Also very unexpected was the binding of the small Au3+ cation exactly between the Watson-Crick sites of a G-C base pair after an obligatory deprotonation of N1 of the guanine base. This extensive study of metal ion binding using X-ray crystallography significantly enriches our knowledge on the binding of middleweight or heavy metal ions to RNA, particularly compared with magnesium.

About this Structure

1NLC is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.

Reference

A crystallographic study of the binding of 13 metal ions to two related RNA duplexes., Ennifar E, Walter P, Dumas P, Nucleic Acids Res. 2003 May 15;31(10):2671-82. PMID:12736317

Page seeded by OCA on Thu Feb 21 14:07:23 2008

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nlc"
Personal tools