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2ytz

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Revision as of 09:11, 17 October 2018

Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein in the orthorhombic crystal-lattice

Structural highlights

2ytz is a 2 chain structure with sequence from 'pyrococcus shinkaii'. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	2dul, 2ejt, 2eju
Gene:	trm1 ('Pyrococcus shinkaii')
Activity:	Transferase, with EC number 2.1.1.214, 2.1.1.215 and 2.1.1.216 2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[TRM1_PYRHO] Dimethylates a single guanine residue at position 26 of a number of tRNAs using S-adenosyl-L-methionine as donor of the methyl groups (By similarity).

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

↑ 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

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein in the orthorhombic crystal-lattice==
 <StructureSection load='2ytz' size='340' side='right' caption='[[2ytz]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='gene'><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 shinkaii'])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216 2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216] </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=2ytz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ytz OCA], [http://pdbe.org/2ytz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ytz RCSB], [http://www.ebi.ac.uk/pdbsum/2ytz PDBsum], [http://www.topsan.org/Proteins/RSGI/2ytz 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=2ytz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ytz OCA], [http://pdbe.org/2ytz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ytz RCSB], [http://www.ebi.ac.uk/pdbsum/2ytz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ytz ProSAT], [http://www.topsan.org/Proteins/RSGI/2ytz TOPSAN]</span></td></tr>
 </table>
 == Function ==
@@ Line 15: / Line 16: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yt/2ytz_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yt/2ytz_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

2ytz

From Proteopedia

Revision as of 09:11, 17 October 2018

Complex structure of Trm1 from Pyrococcus horikoshii with S-adenosyl-L-Homocystein in the orthorhombic crystal-lattice

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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