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5tl4

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Current revision (14:20, 6 March 2024) (edit) (undo)
 
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<StructureSection load='5tl4' size='340' side='right'caption='[[5tl4]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
<StructureSection load='5tl4' size='340' side='right'caption='[[5tl4]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5tl4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_devorans"_zimmermann_1890 "bacillus devorans" zimmermann 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TL4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TL4 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5tl4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TL4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TL4 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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]] 1.751&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ligM ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13689 "Bacillus devorans" Zimmermann 1890])</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</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=5tl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tl4 OCA], [http://pdbe.org/5tl4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tl4 RCSB], [http://www.ebi.ac.uk/pdbsum/5tl4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tl4 ProSAT]</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=5tl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tl4 OCA], [https://pdbe.org/5tl4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tl4 RCSB], [https://www.ebi.ac.uk/pdbsum/5tl4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tl4 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/LIGM_SPHSK LIGM_SPHSK] Involved in the catabolism of vanillate and syringate. Catalyzes the transfer of a methyl moiety from vanillate or 3-O-methylgallate (3MGA) to tetrahydrofolate, forming protocatechuate (PCA) or gallate, respectively, and methyl-tetrahydrofolate. Has similar activities with both substrates (PubMed:15743951). Cannot use syringate (PubMed:15743951). Uses an ordered, sequential kinetic mechanism (PubMed:28373573).<ref>PMID:15743951</ref> <ref>PMID:28373573</ref>
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Some strains of soil and marine bacteria have evolved intricate metabolic pathways for using environmentally derived aromatics as a carbon source. Many of these metabolic pathways go through intermediates such as vanillate, 3-O-methylgallate, and syringate. Demethylation of these compounds is essential for downstream aryl modification, ring opening, and subsequent assimilation of these compounds into the tricarboxylic acid (TCA) cycle, and, correspondingly, there are a variety of associated aryl demethylase systems that vary in complexity. Intriguingly, only a basic understanding of the least complex system, the tetrahydrofolate-dependent aryl demethylase LigM from Sphingomonas paucimobilis, a bacterial strain that metabolizes lignin-derived aromatics, was previously available. LigM-catalyzed demethylation enables further modification and ring opening of the single-ring aromatics vanillate and 3-O-methylgallate, which are common byproducts of biofuel production. Here, we characterize aryl O-demethylation by LigM and report its 1.81-A crystal structure, revealing a unique demethylase fold and a canonical folate-binding domain. Structural homology and geometry optimization calculations enabled the identification of LigM's tetrahydrofolate-binding site and protein-folate interactions. Computationally guided mutagenesis and kinetic analyses allowed the identification of the enzyme's aryl-binding site location and determination of its unique, catalytic tyrosine-dependent reaction mechanism. This work defines LigM as a distinct demethylase, both structurally and functionally, and provides insight into demethylation and its reaction requirements. These results afford the mechanistic details required for efficient utilization of LigM as a tool for aryl O-demethylation and as a component of synthetic biology efforts to valorize previously underused aromatic compounds.
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Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism.,Kohler AC, Mills MJ, Adams PD, Simmons BA, Sale KL Proc Natl Acad Sci U S A. 2017 Apr 3. pii: 201619263. doi:, 10.1073/pnas.1619263114. PMID:28373573<ref>PMID:28373573</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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<div class="pdbe-citations 5tl4" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus devorans zimmermann 1890]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Adams, P D]]
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[[Category: Sphingomonas paucimobilis]]
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[[Category: Kohler, A C]]
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[[Category: Adams PD]]
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[[Category: Sale, K L]]
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[[Category: Kohler AC]]
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[[Category: Simmons, B A]]
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[[Category: Sale KL]]
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[[Category: Aryl]]
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[[Category: Simmons BA]]
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[[Category: Demethylase]]
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[[Category: Tetrahydrofolate-dependent]]
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[[Category: Transferase]]
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Current revision

Crystal structure of Sphingomonas paucimobilis aryl O-demethylase LigM

PDB ID 5tl4

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