3ay0

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine

Structural highlights

3ay0 is a 2 chain structure with sequence from Methanocaldococcus jannaschii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.05Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Publication Abstract from PubMed

Bacterial TrmD and eukaryotic-archaeal Trm5 form a pair of analogous tRNA methyltransferase that catalyze methyl transfer from S-adenosyl methionine (AdoMet) to N(1) of G37, using catalytic motifs that share no sequence or structural homology. Here we show that natural and synthetic analogs of AdoMet are unable to distinguish TrmD from Trm5. Instead, fragments of AdoMet, adenosine and methionine, are selectively inhibitory of TrmD rather than Trm5. Detailed structural information of the two enzymes in complex with adenosine reveals how Trm5 escapes targeting by adopting an altered structure, whereas TrmD is trapped by targeting due to its rigid structure that stably accommodates the fragment. Free energy analysis exposes energetic disparities between the two enzymes in how they approach the binding of AdoMet versus fragments and provides insights into the design of inhibitors selective for TrmD.

Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.,Lahoud G, Goto-Ito S, Yoshida K, Ito T, Yokoyama S, Hou YM RNA. 2011 Jul;17(7):1236-46. Epub 2011 May 20. PMID:21602303^[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
↑ Lahoud G, Goto-Ito S, Yoshida K, Ito T, Yokoyama S, Hou YM. Differentiating analogous tRNA methyltransferases by fragments of the methyl donor. RNA. 2011 Jul;17(7):1236-46. Epub 2011 May 20. PMID:21602303 doi:10.1261/rna.2706011

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ay0"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine==
-<StructureSection load='3ay0' size='340' side='right' caption='[[3ay0]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
+<StructureSection load='3ay0' size='340' side='right'caption='[[3ay0]], [[Resolution|resolution]] 3.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ay0]] 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=3AY0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AY0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ay0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AY0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AY0 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.05&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3axz|3axz]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADN:ADENOSINE'>ADN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ0883, Trm5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 Methanocaldococcus jannaschii])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ay0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ay0 OCA], [https://pdbe.org/3ay0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ay0 RCSB], [https://www.ebi.ac.uk/pdbsum/3ay0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ay0 ProSAT]</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=3ay0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ay0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ay0 RCSB], [http://www.ebi.ac.uk/pdbsum/3ay0 PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 14: / Line 16: @@
 Differentiating analogous tRNA methyltransferases by fragments of the methyl donor.,Lahoud G, Goto-Ito S, Yoshida K, Ito T, Yokoyama S, Hou YM RNA. 2011 Jul;17(7):1236-46. Epub 2011 May 20. PMID:21602303<ref>PMID:21602303</ref>
-From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3ay0" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Methanocaldococcus jannaschii]]
-[[Category: Goto-Ito, S.]]
+[[Category: Goto-Ito S]]
-[[Category: Hou, Y M.]]
+[[Category: Hou YM]]
-[[Category: Ito, T.]]
+[[Category: Ito T]]
-[[Category: Yokoyama, S.]]
+[[Category: Yokoyama S]]
-[[Category: Adomet binding]]
-[[Category: Methyltransferase]]
-[[Category: Rossmann fold]]
-[[Category: Transferase]]

3ay0

From Proteopedia

Current revision

Crystal structure of Methanocaldococcus jannaschii Trm5 in complex with adenosine

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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