5x1k - Revision history

OCA at 07:52, 22 November 2023

OCA — Wed, 22 Nov 2023 07:52:54 GMT

←Older revision		Revision as of 07:52, 22 November 2023
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	<StructureSection load='5x1k' size='340' side='right'caption='[[5x1k]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5x1k' size='340' side='right'caption='[[5x1k]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x1k]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X1K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x1k]] 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=5X1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X1K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7WR:3-METHOXY-4,5-BIS(OXIDANYL)BENZOIC+ACID'>7WR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.15Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x1l\|5x1l]], [[5x1i\|5x1i]], [[5x1j\|5x1j]], [[5x1m\|5x1m]], [[5x1n\|5x1n]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7WR:3-METHOXY-4,5-BIS(OXIDANYL)BENZOIC+ACID'>7WR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5x1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1k OCA], [~~http~~://pdbe.org/5x1k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x1k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x1k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1k 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=5x1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1k OCA], [https://pdbe.org/5x1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x1k RCSB], [https://www.ebi.ac.uk/pdbsum/5x1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1k 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~~]]	+

OCA at 07:22, 7 October 2020

OCA — Wed, 07 Oct 2020 07:22:07 GMT

←Older revision		Revision as of 07:22, 7 October 2020
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	==Vanillate/3-O-methylgallate O-demethylase, LigM, 3-O-methylgallate complex form==		==Vanillate/3-O-methylgallate O-demethylase, LigM, 3-O-methylgallate complex form==
-	<StructureSection load='5x1k' size='340' side='right' caption='[[5x1k]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5x1k' size='340' side='right'caption='[[5x1k]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x1k]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1K OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X1K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x1k]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X1K FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7WR:3-METHOXY-4,5-BIS(OXIDANYL)BENZOIC+ACID'>7WR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7WR:3-METHOXY-4,5-BIS(OXIDANYL)BENZOIC+ACID'>7WR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x1l\|5x1l]], [[5x1i\|5x1i]], [[5x1j\|5x1j]], [[5x1m\|5x1m]], [[5x1n\|5x1n]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x1l\|5x1l]], [[5x1i\|5x1i]], [[5x1j\|5x1j]], [[5x1m\|5x1m]], [[5x1n\|5x1n]]</td></tr>
-	<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=5x1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1k OCA], [http://pdbe.org/5x1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x1k RCSB], [http://www.ebi.ac.uk/pdbsum/5x1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1k ProSAT]</span></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=5x1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1k OCA], [http://pdbe.org/5x1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x1k RCSB], [http://www.ebi.ac.uk/pdbsum/5x1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Harada, A]]		[[Category: Harada, A]]
	[[Category: Senda, T]]		[[Category: Senda, T]]

OCA at 10:30, 3 August 2017

OCA — Thu, 03 Aug 2017 10:30:55 GMT

←Older revision		Revision as of 10:30, 3 August 2017
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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=5x1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1k OCA], [http://pdbe.org/5x1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x1k RCSB], [http://www.ebi.ac.uk/pdbsum/5x1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1k ProSAT]</span></td></tr>		<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=5x1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1k OCA], [http://pdbe.org/5x1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x1k RCSB], [http://www.ebi.ac.uk/pdbsum/5x1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1k ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== 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<ref>PMID:28429420</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5x1k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:51, 17 May 2017

OCA — Wed, 17 May 2017 15:51:42 GMT

←Older revision		Revision as of 15:51, 17 May 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5x1k is ~~ON HOLD until Paper Publication~~	+	==Vanillate/3-O-methylgallate O-demethylase, LigM, 3-O-methylgallate complex form==
-		+	<StructureSection load='5x1k' size='340' side='right' caption='[[5x1k]], [[Resolution\|resolution]] 2.15Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x1k]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X1K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X1K FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=7WR:3-METHOXY-4,5-BIS(OXIDANYL)BENZOIC+ACID'>7WR</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x1l\|5x1l]], [[5x1i\|5x1i]], [[5x1j\|5x1j]], [[5x1m\|5x1m]], [[5x1n\|5x1n]]</td></tr>
		+	<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=5x1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x1k OCA], [http://pdbe.org/5x1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x1k RCSB], [http://www.ebi.ac.uk/pdbsum/5x1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x1k ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Harada, A]]
		+	[[Category: Senda, T]]
		+	[[Category: Lignin]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Sphingobium sp syk-6]]

OCA at 15:34, 9 March 2017

OCA — Thu, 09 Mar 2017 15:34:57 GMT

←Older revision		Revision as of 15:34, 9 March 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x1k is ON HOLD	+	The entry 5x1k is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5x1k" [edit=sysop:move=sysop]

OCA — Wed, 01 Feb 2017 17:11:02 GMT

Protected "5x1k" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:11, 1 February 2017

OCA: New page: '''Unreleased structure''' The entry 5x1k is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 01 Feb 2017 17:11:01 GMT

New page: '''Unreleased structure''' The entry 5x1k is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5x1k is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]