2eju: Difference between revisions

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[[Image:2eju.png|left|200px]]
==Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein==
<StructureSection load='2eju' size='340' side='right' caption='[[2eju]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2eju]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EJU FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2dul|2dul]], [[2ejt|2ejt]]</td></tr>
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">trm1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(guanine-N(2)-)-methyltransferase tRNA (guanine-N(2)-)-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.32 2.1.1.32] </span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2eju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eju OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2eju RCSB], [http://www.ebi.ac.uk/pdbsum/2eju PDBsum], [http://www.topsan.org/Proteins/RSGI/2eju TOPSAN]</span></td></tr>
<table>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ej/2eju_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <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].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Trm1 catalyzes a two-step reaction, leading to mono- and dimethylation of guanosine at position 26 in most eukaryotic and archaeal tRNAs. We report the crystal structures of Trm1 from Pyrococcus horikoshii liganded with S-adenosyl-l-methionine or S-adenosyl-l-homocysteine. The protein comprises N-terminal and C-terminal domains with class I methyltransferase and novel folds, respectively. The methyl moiety of S-adenosyl-l-methionine points toward the invariant Phe27 and Phe140 within a narrow pocket, where the target G26 might flip in. Mutagenesis of Phe27 or Phe140 to alanine abolished the enzyme activity, indicating their role in methylating G26. Structural analyses revealed that the movements of Phe140 and the loop preceding Phe27 may be involved in dissociation of the monomethylated tRNA*Trm1 complex prior to the second methylation. Moreover, the catalytic residues Asp138, Pro139, and Phe140 are in a different motif from that in DNA 6-methyladenosine methyltransferases, suggesting a different methyl transfer mechanism in the Trm1 family.


{{STRUCTURE_2eju|  PDB=2eju  |  SCENE=  }}
Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii.,Ihsanawati, Nishimoto M, Higashijima K, Shirouzu M, Grosjean H, Bessho Y, Yokoyama S J Mol Biol. 2008 Nov 21;383(4):871-84. Epub 2008 Sep 5. PMID:18789948<ref>PMID:18789948</ref>


===Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_18789948}}
== References ==
 
<references/>
==About this Structure==
__TOC__
[[2eju]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EJU OCA].
</StructureSection>
 
==Reference==
<ref group="xtra">PMID:018789948</ref><references group="xtra"/>
[[Category: Pyrococcus horikoshii]]
[[Category: Pyrococcus horikoshii]]
[[Category: Bessho, Y.]]
[[Category: Bessho, Y.]]

Revision as of 05:58, 30 September 2014

Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-HomocysteinComplex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein

Structural highlights

2eju is a 1 chain structure with sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
Related:2dul, 2ejt
Gene:trm1 (Pyrococcus horikoshii)
Activity:tRNA (guanine-N(2)-)-methyltransferase, with EC number 2.1.1.32
Resources:FirstGlance, OCA, RCSB, PDBsum, TOPSAN

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

Trm1 catalyzes a two-step reaction, leading to mono- and dimethylation of guanosine at position 26 in most eukaryotic and archaeal tRNAs. We report the crystal structures of Trm1 from Pyrococcus horikoshii liganded with S-adenosyl-l-methionine or S-adenosyl-l-homocysteine. The protein comprises N-terminal and C-terminal domains with class I methyltransferase and novel folds, respectively. The methyl moiety of S-adenosyl-l-methionine points toward the invariant Phe27 and Phe140 within a narrow pocket, where the target G26 might flip in. Mutagenesis of Phe27 or Phe140 to alanine abolished the enzyme activity, indicating their role in methylating G26. Structural analyses revealed that the movements of Phe140 and the loop preceding Phe27 may be involved in dissociation of the monomethylated tRNA*Trm1 complex prior to the second methylation. Moreover, the catalytic residues Asp138, Pro139, and Phe140 are in a different motif from that in DNA 6-methyladenosine methyltransferases, suggesting a different methyl transfer mechanism in the Trm1 family.

Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii.,Ihsanawati, Nishimoto M, Higashijima K, Shirouzu M, Grosjean H, Bessho Y, Yokoyama S J Mol Biol. 2008 Nov 21;383(4):871-84. Epub 2008 Sep 5. PMID:18789948[1]

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

References

  1. ↑ Ihsanawati, Nishimoto M, Higashijima K, Shirouzu M, Grosjean H, Bessho Y, Yokoyama S. Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii. J Mol Biol. 2008 Nov 21;383(4):871-84. Epub 2008 Sep 5. PMID:18789948 doi:10.1016/j.jmb.2008.08.068

2eju, resolution 1.95Å

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