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4gek

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==Crystal Structure of wild-type CmoA from E.coli==
==Crystal Structure of wild-type CmoA from E.coli==
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<StructureSection load='4gek' size='340' side='right' caption='[[4gek]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
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<StructureSection load='4gek' size='340' side='right'caption='[[4gek]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4gek]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_uti89 Escherichia coli uti89]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GEK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GEK FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4gek]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_str._K-12_substr._MG1655 Escherichia coli str. K-12 substr. MG1655]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GEK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GEK FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cmoA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=364106 Escherichia coli UTI89])</td></tr>
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<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=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<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=4gek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gek OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gek RCSB], [http://www.ebi.ac.uk/pdbsum/4gek PDBsum]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4gek FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gek OCA], [https://pdbe.org/4gek PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gek RCSB], [https://www.ebi.ac.uk/pdbsum/4gek PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gek ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/C3T5M2_ECOLX C3T5M2_ECOLX] Catalyzes the conversion of S-adenosyl-L-methionine (SAM) to carboxy-S-adenosyl-L-methionine (Cx-SAM).[HAMAP-Rule:MF_01589]
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The identification of novel metabolites and the characterization of their biological functions are major challenges in biology. X-ray crystallography can reveal unanticipated ligands that persist through purification and crystallization. These adventitious protein-ligand complexes provide insights into new activities, pathways and regulatory mechanisms. We describe a new metabolite, carboxy-S-adenosyl-l-methionine (Cx-SAM), its biosynthetic pathway and its role in transfer RNA modification. The structure of CmoA, a member of the SAM-dependent methyltransferase superfamily, revealed a ligand consistent with Cx-SAM in the catalytic site. Mechanistic analyses showed an unprecedented role for prephenate as the carboxyl donor and the involvement of a unique ylide intermediate as the carboxyl acceptor in the CmoA-mediated conversion of SAM to Cx-SAM. A second member of the SAM-dependent methyltransferase superfamily, CmoB, recognizes Cx-SAM and acts as a carboxymethyltransferase to convert 5-hydroxyuridine into 5-oxyacetyl uridine at the wobble position of multiple tRNAs in Gram-negative bacteria, resulting in expanded codon-recognition properties. CmoA and CmoB represent the first documented synthase and transferase for Cx-SAM. These findings reveal new functional diversity in the SAM-dependent methyltransferase superfamily and expand the metabolic and biological contributions of SAM-based biochemistry. These discoveries highlight the value of structural genomics approaches in identifying ligands within the context of their physiologically relevant macromolecular binding partners, and in revealing their functions.
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Structure-guided discovery of the metabolite carboxy-SAM that modulates tRNA function.,Kim J, Xiao H, Bonanno JB, Kalyanaraman C, Brown S, Tang X, Al-Obaidi NF, Patskovsky Y, Babbitt PC, Jacobson MP, Lee YS, Almo SC Nature. 2013 May 15. doi: 10.1038/nature12180. PMID:23676670<ref>PMID:23676670</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==See Also==
==See Also==
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*[[TRNA methyltransferase|TRNA methyltransferase]]
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*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Escherichia coli uti89]]
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[[Category: Escherichia coli str. K-12 substr. MG1655]]
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[[Category: Almo, S C]]
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[[Category: Large Structures]]
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[[Category: Bhosle, R]]
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[[Category: Almo SC]]
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[[Category: Bonanno, J B]]
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[[Category: Bhosle R]]
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[[Category: Kim, J]]
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[[Category: Bonanno JB]]
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[[Category: Structural genomic]]
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[[Category: Kim J]]
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[[Category: Sampathkumar, P]]
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[[Category: Sampathkumar P]]
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[[Category: Toro, R]]
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[[Category: Toro R]]
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[[Category: Nysgrc]]
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[[Category: Psi-biology]]
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[[Category: Rossmann fold]]
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[[Category: Sam prephenate]]
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[[Category: Synthase]]
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[[Category: Transferase]]
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Current revision

Crystal Structure of wild-type CmoA from E.coli

PDB ID 4gek

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