2c06
From Proteopedia
(New page: 200px<br /><applet load="2c06" size="450" color="white" frame="true" align="right" spinBox="true" caption="2c06" /> '''NMR-BASED MODEL OF THE COMPLEX OF THE TOXIN ...) |
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| - | [[Image:2c06.gif|left|200px]]<br /><applet load="2c06" size=" | + | [[Image:2c06.gif|left|200px]]<br /><applet load="2c06" size="350" color="white" frame="true" align="right" spinBox="true" |
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'''NMR-BASED MODEL OF THE COMPLEX OF THE TOXIN KID AND A 5-NUCLEOTIDE SUBSTRATE RNA FRAGMENT (AUACA)'''<br /> | '''NMR-BASED MODEL OF THE COMPLEX OF THE TOXIN KID AND A 5-NUCLEOTIDE SUBSTRATE RNA FRAGMENT (AUACA)'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The toxin Kid and antitoxin Kis are encoded by the parD operon of | + | The toxin Kid and antitoxin Kis are encoded by the parD operon of Escherichia coli plasmid R1. Kid and its chromosomal homologues MazF and ChpBK have been shown to inhibit protein synthesis in cell extracts and to act as ribosome-independent endoribonucleases in vitro. Kid cleaves RNA preferentially at the 5' side of the A residue in the nucleotide sequence 5'-UA(A/C)-3' of single-stranded regions. Here, we show that RNA cleavage by Kid yields two fragments with a 2':3'-cyclic phosphate group and a free 5'-OH group, respectively. The cleavage mechanism is similar to that of RNases A and T1, involving the uracil 2'-OH group. Via NMR titration studies with an uncleavable RNA mimic, we demonstrate that residues of both monomers of the Kid dimer together form a concatenated RNA-binding surface. Docking calculations based on the NMR chemical shifts, the cleavage mechanism and previously reported mutagenesis data provide a detailed picture of the position of the AUACA fragment within the binding pocket. We propose that residues D75, R73 and H17 form the active site of the Kid toxin, where D75 and R73 are the catalytic base and acid, respectively. The RNA sequence specificity is defined by residues T46, S47, A55, F57, T69, V71 and R73. Our data show the importance of these residues for Kid function, and the implications of our results for related toxins, such as MazF, CcdB and RelE, are discussed. |
==About this Structure== | ==About this Structure== | ||
| - | 2C06 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http:// | + | 2C06 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C06 OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Boelens, R.]] | [[Category: Boelens, R.]] | ||
| - | [[Category: Bonvin, A | + | [[Category: Bonvin, A M.J J.]] |
[[Category: Diaz-Orejas, R.]] | [[Category: Diaz-Orejas, R.]] | ||
| - | [[Category: Heuvel, R | + | [[Category: Heuvel, R H.H Van Den.]] |
| - | [[Category: Kamphuis, M | + | [[Category: Kamphuis, M B.]] |
[[Category: Lemonnier, M.]] | [[Category: Lemonnier, M.]] | ||
| - | [[Category: Monti, M | + | [[Category: Monti, M C.]] |
[[Category: Munoz-Gomez, A.]] | [[Category: Munoz-Gomez, A.]] | ||
[[Category: dna replication]] | [[Category: dna replication]] | ||
| Line 33: | Line 33: | ||
[[Category: toxin-antitoxin]] | [[Category: toxin-antitoxin]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:43:32 2008'' |
Revision as of 14:43, 21 February 2008
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NMR-BASED MODEL OF THE COMPLEX OF THE TOXIN KID AND A 5-NUCLEOTIDE SUBSTRATE RNA FRAGMENT (AUACA)
Overview
The toxin Kid and antitoxin Kis are encoded by the parD operon of Escherichia coli plasmid R1. Kid and its chromosomal homologues MazF and ChpBK have been shown to inhibit protein synthesis in cell extracts and to act as ribosome-independent endoribonucleases in vitro. Kid cleaves RNA preferentially at the 5' side of the A residue in the nucleotide sequence 5'-UA(A/C)-3' of single-stranded regions. Here, we show that RNA cleavage by Kid yields two fragments with a 2':3'-cyclic phosphate group and a free 5'-OH group, respectively. The cleavage mechanism is similar to that of RNases A and T1, involving the uracil 2'-OH group. Via NMR titration studies with an uncleavable RNA mimic, we demonstrate that residues of both monomers of the Kid dimer together form a concatenated RNA-binding surface. Docking calculations based on the NMR chemical shifts, the cleavage mechanism and previously reported mutagenesis data provide a detailed picture of the position of the AUACA fragment within the binding pocket. We propose that residues D75, R73 and H17 form the active site of the Kid toxin, where D75 and R73 are the catalytic base and acid, respectively. The RNA sequence specificity is defined by residues T46, S47, A55, F57, T69, V71 and R73. Our data show the importance of these residues for Kid function, and the implications of our results for related toxins, such as MazF, CcdB and RelE, are discussed.
About this Structure
2C06 is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Model for RNA binding and the catalytic site of the RNase Kid of the bacterial parD toxin-antitoxin system., Kamphuis MB, Bonvin AM, Monti MC, Lemonnier M, Munoz-Gomez A, van den Heuvel RH, Diaz-Orejas R, Boelens R, J Mol Biol. 2006 Mar 17;357(1):115-26. Epub 2005 Dec 27. PMID:16413033
Page seeded by OCA on Thu Feb 21 16:43:32 2008
Categories: Escherichia coli | Single protein | Boelens, R. | Bonvin, A M.J J. | Diaz-Orejas, R. | Heuvel, R H.H Van Den. | Kamphuis, M B. | Lemonnier, M. | Monti, M C. | Munoz-Gomez, A. | Dna replication | Docking | Mazf | Plasmid maintenance | Post segregational killing | Protein-rna complex | Ribonuclease | Rna cleavage | Rnase | Toxin | Toxin-antitoxin
