2yx1

From Proteopedia

(Difference between revisions)

Revision as of 21:01, 4 August 2016

Crystal structure of M.jannaschii tRNA m1G37 methyltransferase

Structural highlights

2yx1 is a 2 chain structure with sequence from Atcc 43067. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[TRM5B_METJA] Specifically methylates the N1 position of guanosine-37 in various tRNAs.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Methylation of the N1 atom of guanosine at position 37 in tRNA, the position 3'-adjacent to the anticodon, generates the modified nucleoside m(1)G37. In archaea and eukaryotes, m(1)G37 synthesis is catalyzed by tRNA(m(1)G37)methyltransferase (archaeal or eukaryotic Trm5, a/eTrm5). Here we report the crystal structure of archaeal Trm5 (aTrm5) from Methanocaldococcus jannaschii (formerly known as Methanococcus jannaschii) in complex with the methyl donor analogue at 2.2 A resolution. The crystal structure revealed that the entire protein is composed of three structural domains, D1, D2, and D3. In the a/eTrm5 primary structures, D2 and D3 are highly conserved, while D1 is not conserved. The D3 structure is the Rossmann fold, which is the hallmark of the canonical class-I methyltransferases. The a/eTrm5-defining domain, D2, exhibits structural similarity to some class-I methyltransferases. In contrast, a DALI search with the D1 structure yielded no structural homologues. In the crystal structure, D3 contacts both D1 and D2. The residues involved in the D1:D3 interactions are not conserved, while those participating in the D2:D3 interactions are well conserved. D1 and D2 do not contact each other, and the linker between them is disordered. aTrm5 fragments corresponding to the D1 and D2-D3 regions were prepared in a soluble form. The NMR analysis of the D1 fragment revealed that D1 is well folded by itself, and it did not interact with either the D2-D3 fragment or the tRNA. The NMR analysis of the D2-D3 fragment revealed that it is well folded, independently of D1, and that it interacts with tRNA. Furthermore, the D2-D3 fragment was as active as the full-length enzyme for tRNA methylation. The positive charges on the surface of D2-D3 may be involved in tRNA binding. Therefore, these findings suggest that the interaction between D1 and D3 is not persistent, and that the D2-D3 region plays the major role in tRNA methylation. (c) 2008 Wiley-Liss, Inc.

Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.,Goto-Ito S, Ito T, Ishii R, Muto Y, Bessho Y, Yokoyama S Proteins. 2008 Apr 2;. PMID:18384044^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Christian T, Evilia C, Williams S, Hou YM. Distinct origins of tRNA(m1G37) methyltransferase. J Mol Biol. 2004 Jun 11;339(4):707-19. PMID:15165845 doi:http://dx.doi.org/10.1016/j.jmb.2004.04.025
↑ Christian T, Evilia C, Hou YM. Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline. Biochemistry. 2006 Jun 20;45(24):7463-73. PMID:16768442 doi:http://dx.doi.org/10.1021/bi0602314
↑ Christian T, Lahoud G, Liu C, Hoffmann K, Perona JJ, Hou YM. Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5. RNA. 2010 Dec;16(12):2484-92. doi: 10.1261/rna.2376210. Epub 2010 Oct 27. PMID:20980671 doi:http://dx.doi.org/10.1261/rna.2376210
↑ Goto-Ito S, Ito T, Ishii R, Muto Y, Bessho Y, Yokoyama S. Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5. Proteins. 2008 Apr 2;. PMID:18384044 doi:http://dx.doi.org/10.1002/prot.22019

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2yx1"

@@ Line 1: / Line 1: @@
 ==Crystal structure of M.jannaschii tRNA m1G37 methyltransferase==
 <StructureSection load='2yx1' size='340' side='right' caption='[[2yx1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yx1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YX1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yx1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YX1 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yx1 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx1 PDBsum], [http://www.topsan.org/Proteins/RSGI/2yx1 TOPSAN]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yx1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx1 OCA], [http://pdbe.org/2yx1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yx1 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yx1 ProSAT], [http://www.topsan.org/Proteins/RSGI/2yx1 TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Y883_METJA Y883_METJA]] Specifically methylates the N1 position of guanosine-37 in various tRNAs.<ref>PMID:15165845</ref> <ref>PMID:16768442</ref> <ref>PMID:20980671</ref>
+[[http://www.uniprot.org/uniprot/TRM5B_METJA TRM5B_METJA]] Specifically methylates the N1 position of guanosine-37 in various tRNAs.<ref>PMID:15165845</ref> <ref>PMID:16768442</ref> <ref>PMID:20980671</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 18: @@
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2yx1 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2yx1" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Methanocaldococcus jannaschii]]
+[[Category: Atcc 43067]]
 [[Category: Bessho, Y]]
 [[Category: Goto-Ito, S]]

2yx1

From Proteopedia

Revision as of 21:01, 4 August 2016

Crystal structure of M.jannaschii tRNA m1G37 methyltransferase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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