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| | <StructureSection load='5x1m' size='340' side='right'caption='[[5x1m]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='5x1m' size='340' side='right'caption='[[5x1m]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5x1m]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1M OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X1M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5x1m]] 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=5X1M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X1M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHB:3,4-DIHYDROXYBENZOIC+ACID'>DHB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=THG:(6S)-5,6,7,8-TETRAHYDROFOLATE'>THG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5x1n|5x1n]], [[5x1l|5x1l]], [[5x1k|5x1k]], [[5x1i|5x1i]], [[5x1j|5x1j]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DHB:3,4-DIHYDROXYBENZOIC+ACID'>DHB</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=THG:(6S)-5,6,7,8-TETRAHYDROFOLATE'>THG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5x1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1m OCA], [http://pdbe.org/5x1m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x1m RCSB], [http://www.ebi.ac.uk/pdbsum/5x1m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1m 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=5x1m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1m OCA], [https://pdbe.org/5x1m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x1m RCSB], [https://www.ebi.ac.uk/pdbsum/5x1m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1m ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [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> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Harada, A]] | + | [[Category: Sphingobium sp. SYK-6]] |
| - | [[Category: Senda, T]] | + | [[Category: Harada A]] |
| - | [[Category: Lignin]] | + | [[Category: Senda T]] |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Sphingobium sp. syk-6]]
| + | |
| Structural highlights
Function
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).[1] [2]
Publication Abstract from PubMed
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.
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Abe T, Masai E, Miyauchi K, Katayama Y, Fukuda M. A tetrahydrofolate-dependent O-demethylase, LigM, is crucial for catabolism of vanillate and syringate in Sphingomonas paucimobilis SYK-6. J Bacteriol. 2005 Mar;187(6):2030-7. PMID:15743951 doi:10.1128/JB.187.6.2030-2037.2005
- ↑ Kohler AC, Mills MJ, Adams PD, Simmons BA, Sale KL. Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism. Proc Natl Acad Sci U S A. 2017 Apr 3. pii: 201619263. doi:, 10.1073/pnas.1619263114. PMID:28373573 doi:http://dx.doi.org/10.1073/pnas.1619263114
- ↑ Harada A, Kamimura N, Takeuchi K, Yu HY, Masai E, Senda T. The crystal structure of a new O-demethylase from Sphingobium sp. strain SYK-6. FEBS J. 2017 Jun;284(12):1855-1867. doi: 10.1111/febs.14085. Epub 2017 May 11. PMID:28429420 doi:http://dx.doi.org/10.1111/febs.14085
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