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| | <StructureSection load='3ajd' size='340' side='right'caption='[[3ajd]], [[Resolution|resolution]] 1.27Å' scene=''> | | <StructureSection load='3ajd' size='340' side='right'caption='[[3ajd]], [[Resolution|resolution]] 1.27Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ajd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43067 Atcc 43067]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AJD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ajd]] is a 1 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=3AJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AJD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.27Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3a4t|3a4t]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MJ0026 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2190 ATCC 43067])</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=3ajd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ajd OCA], [https://pdbe.org/3ajd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ajd RCSB], [https://www.ebi.ac.uk/pdbsum/3ajd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ajd ProSAT]</span></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=3ajd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ajd OCA], [https://pdbe.org/3ajd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ajd RCSB], [https://www.ebi.ac.uk/pdbsum/3ajd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ajd ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/TRM4_METJA TRM4_METJA]] Catalyzes AdoMet-dependent formation of m5C in tRNA. Cytidine residue at either position 40 or position 48 is likely to be methylated.<ref>PMID:20600111</ref>
| + | [https://www.uniprot.org/uniprot/TRM4_METJA TRM4_METJA] Catalyzes AdoMet-dependent formation of m5C in tRNA. Cytidine residue at either position 40 or position 48 is likely to be methylated.<ref>PMID:20600111</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43067]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hirano, M]] | + | [[Category: Methanocaldococcus jannaschii]] |
| - | [[Category: Kuratani, M]] | + | [[Category: Hirano M]] |
| - | [[Category: Structural genomic]] | + | [[Category: Kuratani M]] |
| - | [[Category: Yokoyama, S]] | + | [[Category: Yokoyama S]] |
| - | [[Category: M5c]]
| + | |
| - | [[Category: Methyltransferase]]
| + | |
| - | [[Category: National project on protein structural and functional analyse]]
| + | |
| - | [[Category: Nppsfa]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: S-adenosyl-l-methionine]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Trna]]
| + | |
| Structural highlights
Function
TRM4_METJA Catalyzes AdoMet-dependent formation of m5C in tRNA. Cytidine residue at either position 40 or position 48 is likely to be methylated.[1]
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:m(5)C methyltransferase Trm4 generates the modified nucleotide 5-methylcytidine in archaeal and eukaryotic tRNA molecules, using S-adenosyl-l-methionine (AdoMet) as methyl donor. Most archaea and eukaryotes possess several Trm4 homologs, including those related to diseases, while the archaeon Methanocaldococcus jannaschii has only one gene encoding a Trm4 homolog, MJ0026. The recombinant MJ0026 protein catalyzed AdoMet-dependent methyltransferase activity on tRNA in vitro and was shown to be the M. jannaschii Trm4. We determined the crystal structures of the substrate-free M. jannaschii Trm4 and its complex with sinefungin at 1.27 A and 2.3 A resolutions, respectively. This AdoMet analog is bound in a negatively charged pocket near helix alpha8. This helix can adopt two different conformations, thereby controlling the entry of AdoMet into the active site. Adjacent to the sinefungin-bound pocket, highly conserved residues form a large, positively charged surface, which seems to be suitable for tRNA binding. The structure explains the roles of several conserved residues that were reportedly involved in the enzymatic activity or stability of Trm4p from the yeast Saccharomyces cerevisiae. We also discuss previous genetic and biochemical data on human NSUN2/hTrm4/Misu and archaeal PAB1947 methyltransferase, based on the structure of M. jannaschii Trm4.
Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.,Kuratani M, Hirano M, Goto-Ito S, Itoh Y, Hikida Y, Nishimoto M, Sekine S, Bessho Y, Ito T, Grosjean H, Yokoyama S J Mol Biol. 2010 Aug 20;401(3):323-33. Epub 2010 Jun 30. PMID:20600111[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kuratani M, Hirano M, Goto-Ito S, Itoh Y, Hikida Y, Nishimoto M, Sekine S, Bessho Y, Ito T, Grosjean H, Yokoyama S. Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin. J Mol Biol. 2010 Aug 20;401(3):323-33. Epub 2010 Jun 30. PMID:20600111 doi:10.1016/j.jmb.2010.06.046
- ↑ Kuratani M, Hirano M, Goto-Ito S, Itoh Y, Hikida Y, Nishimoto M, Sekine S, Bessho Y, Ito T, Grosjean H, Yokoyama S. Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin. J Mol Biol. 2010 Aug 20;401(3):323-33. Epub 2010 Jun 30. PMID:20600111 doi:10.1016/j.jmb.2010.06.046
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