2zzm: Difference between revisions

Revision as of 12:32, 9 February 2016

The complex structure of aTrm5 and tRNALeu

Structural highlights

2zzm 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:	MG, SAM
NonStd Res:	MLZ
Related:	2zzn
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

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

tRNA precursors undergo a maturation process, involving nucleotide modifications and folding into the L-shaped tertiary structure. The N1-methylguanosine at position 37 (m1G37), 3' adjacent to the anticodon, is essential for translational fidelity and efficiency. In archaea and eukaryotes, Trm5 introduces the m1G37 modification into all tRNAs bearing G37. Here we report the crystal structures of archaeal Trm5 (aTrm5) in complex with tRNA(Leu) or tRNA(Cys). The D2-D3 domains of aTrm5 discover and modify G37, independently of the tRNA sequences. D1 is connected to D2-D3 through a flexible linker and is designed to recognize the shape of the tRNA outer corner, as a hallmark of the completed L shape formation. This interaction by D1 lowers the K(m) value for tRNA, enabling the D2-D3 catalysis. Thus, we propose that aTrm5 provides the tertiary structure checkpoint in tRNA maturation.

Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation.,Goto-Ito S, Ito T, Kuratani M, Bessho Y, Yokoyama S Nat Struct Mol Biol. 2009 Oct;16(10):1109-15. Epub 2009 Sep 13. PMID:19749755^[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:https://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:https://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:https://dx.doi.org/10.1261/rna.2376210
↑ Goto-Ito S, Ito T, Kuratani M, Bessho Y, Yokoyama S. Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Nat Struct Mol Biol. 2009 Oct;16(10):1109-15. Epub 2009 Sep 13. PMID:19749755 doi:10.1038/nsmb.1653

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OCA

[1] 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:https://dx.doi.org/10.1016/j.jmb.2004.04.025

[2] 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:https://dx.doi.org/10.1021/bi0602314

[3] 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:https://dx.doi.org/10.1261/rna.2376210

[4] Goto-Ito S, Ito T, Kuratani M, Bessho Y, Yokoyama S. Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Nat Struct Mol Biol. 2009 Oct;16(10):1109-15. Epub 2009 Sep 13. PMID:19749755 doi:10.1038/nsmb.1653

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[2]

[3]

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@@ Line 2: / Line 2: @@
 <StructureSection load='2zzm' size='340' side='right' caption='[[2zzm]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zzm]] 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=2ZZM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZZM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zzm]] 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=2ZZM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZZM FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2zzn|2zzn]]</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=2zzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zzm RCSB], [http://www.ebi.ac.uk/pdbsum/2zzm PDBsum]</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=2zzm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zzm OCA], [http://pdbe.org/2zzm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zzm RCSB], [http://www.ebi.ac.uk/pdbsum/2zzm PDBsum]</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 18: / 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=2zzm ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2zzm" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Methanocaldococcus jannaschii]]
+[[Category: Atcc 43067]]
 [[Category: Goto-Ito, S]]
 [[Category: Ito, T]]

2zzm: Difference between revisions

Revision as of 12:32, 9 February 2016

The complex structure of aTrm5 and tRNALeu

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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