1v2x
From Proteopedia
(New page: 200px<br /><applet load="1v2x" size="450" color="white" frame="true" align="right" spinBox="true" caption="1v2x, resolution 1.50Å" /> '''TrmH'''<br /> ==Ove...) |
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| - | [[Image:1v2x.jpg|left|200px]]<br /><applet load="1v2x" size=" | + | [[Image:1v2x.jpg|left|200px]]<br /><applet load="1v2x" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1v2x, resolution 1.50Å" /> | caption="1v2x, resolution 1.50Å" /> | ||
'''TrmH'''<br /> | '''TrmH'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of | + | The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 A resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2'-OH group for methylation. |
==About this Structure== | ==About this Structure== | ||
| - | 1V2X is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with PO4 and SAM as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/tRNA_guanosine-2'-O-methyltransferase tRNA guanosine-2'-O-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.34 2.1.1.34] Full crystallographic information is available from [http:// | + | 1V2X is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=SAM:'>SAM</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/tRNA_guanosine-2'-O-methyltransferase tRNA guanosine-2'-O-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.34 2.1.1.34] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V2X OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Ishii, R.]] | [[Category: Ishii, R.]] | ||
[[Category: Nureki, O.]] | [[Category: Nureki, O.]] | ||
| - | [[Category: RSGI, RIKEN | + | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] |
[[Category: Watanabe, K.]] | [[Category: Watanabe, K.]] | ||
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
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[[Category: structural genomics]] | [[Category: structural genomics]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:30:54 2008'' |
Revision as of 13:31, 21 February 2008
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TrmH
Overview
The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2'-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 A resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2'-OH group for methylation.
About this Structure
1V2X is a Single protein structure of sequence from Thermus thermophilus with and as ligands. Active as tRNA guanosine-2'-O-methyltransferase, with EC number 2.1.1.34 Full crystallographic information is available from OCA.
Reference
Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme., Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H, Yokoyama S, Structure. 2004 Apr;12(4):593-602. PMID:15062082
Page seeded by OCA on Thu Feb 21 15:30:54 2008
Categories: Single protein | Thermus thermophilus | TRNA guanosine-2'-O-methyltransferase | Endo, Y. | Fukai, S. | Hori, H. | Ishii, R. | Nureki, O. | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Watanabe, K. | Yokoyama, S. | PO4 | SAM | Deep trefoil knot | Riken structural genomics/proteomics initiative | Rsgi | Structural genomics
