5x1i

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==Vanillate/3-O-methylgallate O-demethylase, LigM, substrate free form==
==Vanillate/3-O-methylgallate O-demethylase, LigM, substrate free form==
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<StructureSection load='5x1i' size='340' side='right' caption='[[5x1i]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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<StructureSection load='5x1i' size='340' side='right'caption='[[5x1i]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5x1i]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X1I FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5x1i]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingobium_sp._SYK-6 Sphingobium sp. SYK-6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X1I 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=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.9&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x1j|5x1j]], [[5x1k|5x1k]], [[5x1l|5x1l]], [[5x1m|5x1m]], [[5x1n|5x1n]]</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=EDO:1,2-ETHANEDIOL'>EDO</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=5x1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1i OCA], [http://pdbe.org/5x1i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x1i RCSB], [http://www.ebi.ac.uk/pdbsum/5x1i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1i 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=5x1i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1i OCA], [https://pdbe.org/5x1i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x1i RCSB], [https://www.ebi.ac.uk/pdbsum/5x1i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1i 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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In the cell, tetrahydrofolate (H4 folate) derivatives with a C1 unit are utilized in various ways, such as for the synthesis of amino acids and nucleic acids. While H4 folate derivatives with the C1 unit are typically produced in the glycine cleavage system, Sphingobium sp. strain SYK-6, which can utilize lignin-derived aromatic compounds as a sole source of carbon and energy, lacks this pathway, probably due to its unique nutrient requirements. In this bacterium, H4 folate-dependent O-demethylases in catabolic pathways for lignin-derived aromatic compounds seem to be involved in the C1 metabolism. LigM is one of the O-demethylases and catalyzes a C1-unit transfer from vanillate (VNL) to H4 folate. As the primary structure of LigM shows a similarity to T-protein in the glycine cleavage system, we hypothesized that LigM has evolved from T-protein, acquiring its unique biochemical and biological functions. To prove this hypothesis, structure-based understanding of its catalytic reaction is essential. Here, we determined the crystal structure of LigM in apo form and in complex with substrates and H4 folate. These crystal structures showed that the overall structure of LigM is similar to T-protein, but LigM has a few distinct characteristics, particularly in the active site. Structure-based mutational analysis revealed that His60 and Tyr247, which are not conserved in T-protein, are essential to the catalytic activity of LigM and their interactions with the oxygen atom in the methoxy group of VNL seem to facilitate a methyl moiety (C1-unit) transfer to H4 folate. Taken together, our structural data suggest that LigM has evolved divergently from T-protein. DATABASES: All atomic coordinates of the crystal structures determined in this study have been deposited to PDB. LigM: 5X1I, LigM-VNL complex: 5X1J, LigM-3-O-methylgallate complex: 5X1K, LigM-H4 folate complex: 5X1IL, LigM-H4 folate-protocatechuate (PCA) complex (P21 21 2): 5X1M, LigM-H4 folate-PCA complex (P31 21): 5X1N.
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The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6.,Harada A, Kamimura N, Takeuchi K, Yu HY, Masai E, Senda T FEBS J. 2017 Jun;284(12):1855-1867. doi: 10.1111/febs.14085. Epub 2017 May 11. PMID:28429420<ref>PMID:28429420</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 5x1i" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Harada, A]]
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[[Category: Large Structures]]
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[[Category: Senda, T]]
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[[Category: Sphingobium sp. SYK-6]]
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[[Category: Lignin]]
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[[Category: Harada A]]
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[[Category: Oxidoreductase]]
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[[Category: Senda T]]
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[[Category: Sphingobium sp. syk-6]]
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Current revision

Vanillate/3-O-methylgallate O-demethylase, LigM, substrate free form

PDB ID 5x1i

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