2frx
From Proteopedia
(New page: 200px<br /><applet load="2frx" size="450" color="white" frame="true" align="right" spinBox="true" caption="2frx, resolution 2.900Å" /> '''Crystal structure o...) |
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| - | [[Image:2frx.gif|left|200px]]<br /><applet load="2frx" size=" | + | [[Image:2frx.gif|left|200px]]<br /><applet load="2frx" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2frx, resolution 2.900Å" /> | caption="2frx, resolution 2.900Å" /> | ||
'''Crystal structure of YebU, a m5C RNA methyltransferase from E.coli'''<br /> | '''Crystal structure of YebU, a m5C RNA methyltransferase from E.coli'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Nucleotide methylations are the most common type of rRNA modification in | + | Nucleotide methylations are the most common type of rRNA modification in bacteria, and are introduced post-transcriptionally by a wide variety of site-specific enzymes. Three 5-methylcytidine (m(5)C) bases are found in the rRNAs of Escherichia coli and one of these, at nucleotide 1407 in 16 S rRNA, is the modification product of the methyltransferase (MTase) YebU (also called RsmF). YebU requires S-adenosyl-l-methionine (SAM) and methylates C1407 within assembled 30 S subunits, but not in naked 16 S rRNA or within tight-couple 70 S ribosomes. Here, we describe the three-dimensional structure of YebU determined by X-ray crystallography, and we present a molecular model for how YebU specifically recognizes, binds and methylates its ribosomal substrate. The YebU protein has an N-terminal SAM-binding catalytic domain with structural similarity to the equivalent domains in several other m(5)C RNA MTases including RsmB and PH1374. The C-terminal one-third of YebU contains a domain similar to that in pseudouridine synthases and archaeosine-specific transglycosylases (PUA-domain), which was not predicted by sequence alignments. Furthermore, YebU is predicted to contain extended regions of positive electrostatic potential that differ from other RNA-MTase structures, suggesting that YebU interacts with its RNA target in a different manner. Docking of YebU onto the 30 S subunit indicates that the PUA and MTase domains make several contacts with 16 S rRNA as well as with the ribosomal protein S12. The ribosomal protein interactions would explain why the assembled 30 S subunit, and not naked 16 S rRNA, is the preferred substrate for YebU. |
==About this Structure== | ==About this Structure== | ||
| - | 2FRX 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:// | + | 2FRX 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=2FRX OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Ericsson, U | + | [[Category: Ericsson, U B.]] |
[[Category: Erlandsen, H.]] | [[Category: Erlandsen, H.]] | ||
| - | [[Category: Hallberg, B | + | [[Category: Hallberg, B M.]] |
| - | [[Category: Johnson, K | + | [[Category: Johnson, K A.]] |
[[Category: Nordlund, P.]] | [[Category: Nordlund, P.]] | ||
[[Category: c-terminal pua (pseudouridine synthases and archaeosine-specific transglycosylases) domain]] | [[Category: c-terminal pua (pseudouridine synthases and archaeosine-specific transglycosylases) domain]] | ||
[[Category: rossmann-type s-adenosylmethionine-dependent methyltransferase domain]] | [[Category: rossmann-type s-adenosylmethionine-dependent methyltransferase domain]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:24:29 2008'' |
Revision as of 15:24, 21 February 2008
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Crystal structure of YebU, a m5C RNA methyltransferase from E.coli
Overview
Nucleotide methylations are the most common type of rRNA modification in bacteria, and are introduced post-transcriptionally by a wide variety of site-specific enzymes. Three 5-methylcytidine (m(5)C) bases are found in the rRNAs of Escherichia coli and one of these, at nucleotide 1407 in 16 S rRNA, is the modification product of the methyltransferase (MTase) YebU (also called RsmF). YebU requires S-adenosyl-l-methionine (SAM) and methylates C1407 within assembled 30 S subunits, but not in naked 16 S rRNA or within tight-couple 70 S ribosomes. Here, we describe the three-dimensional structure of YebU determined by X-ray crystallography, and we present a molecular model for how YebU specifically recognizes, binds and methylates its ribosomal substrate. The YebU protein has an N-terminal SAM-binding catalytic domain with structural similarity to the equivalent domains in several other m(5)C RNA MTases including RsmB and PH1374. The C-terminal one-third of YebU contains a domain similar to that in pseudouridine synthases and archaeosine-specific transglycosylases (PUA-domain), which was not predicted by sequence alignments. Furthermore, YebU is predicted to contain extended regions of positive electrostatic potential that differ from other RNA-MTase structures, suggesting that YebU interacts with its RNA target in a different manner. Docking of YebU onto the 30 S subunit indicates that the PUA and MTase domains make several contacts with 16 S rRNA as well as with the ribosomal protein S12. The ribosomal protein interactions would explain why the assembled 30 S subunit, and not naked 16 S rRNA, is the preferred substrate for YebU.
About this Structure
2FRX is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain., Hallberg BM, Ericsson UB, Johnson KA, Andersen NM, Douthwaite S, Nordlund P, Beuscher AE 4th, Erlandsen H, J Mol Biol. 2006 Jul 21;360(4):774-87. Epub 2006 Jun 6. PMID:16793063
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