4qnu: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4qnu]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_APEC_O1 Escherichia coli APEC O1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QNU FirstGlance]. <br>
<table><tr><td colspan='2'>[[4qnu]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_APEC_O1 Escherichia coli APEC O1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QNU FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GEK:(2S)-4-[{[(2S,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL}(CARBOXYLATOMETHYL)SULFONIO]-2-AMMONIOBUTANOATE'>GEK</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GEK:(2S)-4-[{[(2S,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL}(CARBOXYLATOMETHYL)SULFONIO]-2-AMMONIOBUTANOATE'>GEK</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=4qnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qnu OCA], [https://pdbe.org/4qnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qnu RCSB], [https://www.ebi.ac.uk/pdbsum/4qnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qnu 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=4qnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qnu OCA], [https://pdbe.org/4qnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qnu RCSB], [https://www.ebi.ac.uk/pdbsum/4qnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qnu ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/CMOB_ECOK1 CMOB_ECOK1] Catalyzes the conversion of 5-hydroxyuridine (ho5U) to 5-methoxyuridine (mo5U) at position 34 in tRNA.[HAMAP-Rule:MF_01590]
[https://www.uniprot.org/uniprot/CMOB_ECOK1 CMOB_ECOK1] Catalyzes the conversion of 5-hydroxyuridine (ho5U) to 5-methoxyuridine (mo5U) at position 34 in tRNA.[HAMAP-Rule:MF_01590]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Enzyme-mediated modifications at the wobble position of tRNAs are essential for the translation of the genetic code. We report the genetic, biochemical and structural characterization of CmoB, the enzyme that recognizes the unique metabolite carboxy-S-adenosine-L-methionine (Cx-SAM) and catalyzes a carboxymethyl transfer reaction resulting in formation of 5-oxyacetyluridine at the wobble position of tRNAs. CmoB is distinctive in that it is the only known member of the SAM-dependent methyltransferase (SDMT) superfamily that utilizes a naturally occurring SAM analog as the alkyl donor to fulfill a biologically meaningful function. Biochemical and genetic studies define the in vitro and in vivo selectivity for Cx-SAM as alkyl donor over the vastly more abundant SAM. Complementary high-resolution structures of the apo- and Cx-SAM bound CmoB reveal the determinants responsible for this remarkable discrimination. Together, these studies provide mechanistic insight into the enzymatic and non-enzymatic feature of this alkyl transfer reaction which affords the broadened specificity required for tRNAs to recognize multiple synonymous codons.
Determinants of the CmoB carboxymethyl transferase utilized for selective tRNA wobble modification.,Kim J, Xiao H, Koh J, Wang Y, Bonanno JB, Thomas K, Babbitt PC, Brown S, Lee YS, Almo SC Nucleic Acids Res. 2015 Apr 8. pii: gkv206. PMID:25855808<ref>PMID:25855808</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4qnu" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Latest revision as of 12:47, 1 March 2024

Crystal structure of CmoB bound with Cx-SAM in P21212

4qnu, resolution 2.60Å

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