8joz: Difference between revisions

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<table><tr><td colspan='2'>[[8joz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8JOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8JOZ FirstGlance]. <br>
<table><tr><td colspan='2'>[[8joz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8JOZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8JOZ FirstGlance]. <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]] 2.22&#8491;</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]] 2.22&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=CM0:5-(CARBOXYMETHOXY)+URIDINE-5-MONOPHOSPHATE'>CM0</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene>, <scene name='pdbligand=ZJS:N-(3-methylbut-2-en-1-yl)adenosine+5-(dihydrogen+phosphate)'>ZJS</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=CM0:5-(CARBOXYMETHOXY)+URIDINE-5-MONOPHOSPHATE'>CM0</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene>, <scene name='pdbligand=ZJS:[(2~{R},3~{S},4~{R},5~{R})-5-[6-(3-methylbut-2-enylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>ZJS</scene></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=8joz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8joz OCA], [https://pdbe.org/8joz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8joz RCSB], [https://www.ebi.ac.uk/pdbsum/8joz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8joz 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=8joz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8joz OCA], [https://pdbe.org/8joz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8joz RCSB], [https://www.ebi.ac.uk/pdbsum/8joz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8joz ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/CMOM_ECOLI CMOM_ECOLI] Catalyzes the methylation of 5-carboxymethoxyuridine (cmo5U) to form 5-methoxycarbonylmethoxyuridine (mcmo5U) at position 34 in tRNAs. Four tRNAs (tRNA(Ala1), tRNA(Ser1), tRNA(Pro3) and tRNA(Thr4)) are fully modified with mcmo5U in stationary-phase E.coli. Also present at low frequency in tRNA(Leu3) and tRNA(Val1).<ref>PMID:26681692</ref>  
[https://www.uniprot.org/uniprot/CMOM_ECOLI CMOM_ECOLI] Catalyzes the methylation of 5-carboxymethoxyuridine (cmo5U) to form 5-methoxycarbonylmethoxyuridine (mcmo5U) at position 34 in tRNAs. Four tRNAs (tRNA(Ala1), tRNA(Ser1), tRNA(Pro3) and tRNA(Thr4)) are fully modified with mcmo5U in stationary-phase E.coli. Also present at low frequency in tRNA(Leu3) and tRNA(Val1).<ref>PMID:26681692</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Posttranscriptional modifications of tRNA are widely conserved in all domains of life. Especially, those occurring within the anticodon often modulate translational efficiency. Derivatives of 5-hydroxyuridine are specifically found in bacterial tRNA, where 5-methoxyuridine and 5-carboxymethoxyuridine are the major species in Gram-positive and Gram-negative bacteria, respectively. In certain tRNA species, 5-carboxymethoxyuridine can be further methylated by CmoM to form the methyl ester. In this report, we present the X-ray crystal structure of Escherichia coli CmoM complexed with tRNASer1, which contains 5-carboxymethoxyuridine at the 5'-end of anticodon (the 34th position of tRNA). The 2.22 A resolution structure of the enzyme-tRNA complex reveals that both the protein and tRNA undergo local conformational changes around the binding interface. Especially, the hypomodified uracil base is flipped out from the canonical stacked conformation enabling the specific molecular interactions with the enzyme. Moreover, the structure illustrates that the enzyme senses exclusively the anticodon arm region of the substrate tRNA and examines the presence of key determinants, 5-carboxymethoxyuridine at position 34 and guanosine at position 35, offering molecular basis for the discriminatory mechanism against non-cognate tRNAs.
Structural basis for the selective methylation of 5-carboxymethoxyuridine in tRNA modification.,Yoo J, Lee J, Kim J Nucleic Acids Res. 2023 Aug 17:gkad668. doi: 10.1093/nar/gkad668. PMID:37587716<ref>PMID:37587716</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8joz" style="background-color:#fffaf0;"></div>
== References ==
== References ==
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Latest revision as of 13:56, 1 July 2026

Crystal structure of CmoM from E. coli complexed with sinefungin and cellularly expressed tRNA Ser

8joz, resolution 2.22Å

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