5l46 - Revision history

OCA at 16:06, 4 October 2023

OCA — Wed, 04 Oct 2023 16:06:27 GMT

←Older revision		Revision as of 16:06, 4 October 2023
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	<StructureSection load='5l46' size='340' side='right'caption='[[5l46]], [[Resolution\|resolution]] 3.09Å' scene=''>		<StructureSection load='5l46' size='340' side='right'caption='[[5l46]], [[Resolution\|resolution]] 3.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l46]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L46 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5L46 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l46]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L46 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</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]] 3.09Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DMGDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Dimethylglycine_dehydrogenase Dimethylglycine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.4 1.5.8.4]~~ </~~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=5l46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l46 OCA], [https://pdbe.org/5l46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l46 RCSB], [https://www.ebi.ac.uk/pdbsum/5l46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l46 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=5l46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l46 OCA], [~~http~~://pdbe.org/5l46 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5l46 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5l46 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5l46 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/M2GD_HUMAN M2GD_HUMAN]] Dimethylglycine dehydrogenase deficiency. The disease is caused by mutations affecting the gene represented in this entry.	+	[https://www.uniprot.org/uniprot/M2GD_HUMAN M2GD_HUMAN] Dimethylglycine dehydrogenase deficiency. The disease is caused by mutations affecting the gene represented in this entry.
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/M2GD_HUMAN M2GD_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dimethylglycine dehydrogenase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gruber, K]]	+	[[Category: Gruber K]]
-	[[Category: Hromic, A]]	+	[[Category: Hromic A]]
-	[[Category: Pavkov-Keller, T]]	+	[[Category: Pavkov-Keller T]]
-	~~[[Category: Covalent flavinylation]]~~	+
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: One-carbon metabolism]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:43, 5 August 2020

OCA — Wed, 05 Aug 2020 06:43:20 GMT

←Older revision		Revision as of 06:43, 5 August 2020
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	==Crystal structure of human dimethylglycine-dehydrogenase==		==Crystal structure of human dimethylglycine-dehydrogenase==
-	<StructureSection load='5l46' size='340' side='right' caption='[[5l46]], [[Resolution\|resolution]] 3.09Å' scene=''>	+	<StructureSection load='5l46' size='340' side='right'caption='[[5l46]], [[Resolution\|resolution]] 3.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l46]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L46 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca.weizmann~~.~~ac.il/oca-docs~~/fgij/fg.htm?mol=5L46 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l46]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L46 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5L46 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DMGDH ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dimethylglycine_dehydrogenase Dimethylglycine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.4 1.5.8.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dimethylglycine_dehydrogenase Dimethylglycine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.4 1.5.8.4] </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=5l46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l46 OCA], [http://pdbe.org/5l46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l46 RCSB], [http://www.ebi.ac.uk/pdbsum/5l46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l46 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=5l46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l46 OCA], [http://pdbe.org/5l46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l46 RCSB], [http://www.ebi.ac.uk/pdbsum/5l46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l46 ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
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	</StructureSection>		</StructureSection>
	[[Category: Dimethylglycine dehydrogenase]]		[[Category: Dimethylglycine dehydrogenase]]
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Gruber, K]]		[[Category: Gruber, K]]
	[[Category: Hromic, A]]		[[Category: Hromic, A]]

OCA at 00:08, 10 September 2016

OCA — Sat, 10 Sep 2016 00:08:03 GMT

←Older revision		Revision as of 00:08, 10 September 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5l46 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of human dimethylglycine-dehydrogenase==
		+	<StructureSection load='5l46' size='340' side='right' caption='[[5l46]], [[Resolution\|resolution]] 3.09Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5l46]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5L46 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dimethylglycine_dehydrogenase Dimethylglycine dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.8.4 1.5.8.4] </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=5l46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l46 OCA], [http://pdbe.org/5l46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l46 RCSB], [http://www.ebi.ac.uk/pdbsum/5l46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l46 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/M2GD_HUMAN M2GD_HUMAN]] Dimethylglycine dehydrogenase deficiency. The disease is caused by mutations affecting the gene represented in this entry.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human dimethylglycine dehydrogenase (hDMGDH) is a flavin adenine dinucleotide (FAD)- and tetrahydrofolate (THF)-dependent, mitochondrial matrix enzyme taking part in choline degradation, one-carbon metabolism and electron transfer to the respiratory chain. The rare natural variant H109R causes dimethylglycine dehydrogenase deficiency leading to increased blood and urinary dimethylglycine concentrations. A detailed biochemical and structural characterization of hDMGDH was thus far hampered by insufficient heterologous expression of the protein. In the present study, we report the development of an intracellular, heterologous expression system in Komagataella phaffii (formerly known as Pichia pastoris) providing the opportunity to determine kinetic parameters, spectroscopic properties, thermostability, and the redox potential of hDMGDH. Moreover, we have successfully crystallized the wild-type enzyme and determined the structure to 3.1-A resolution. The structure-based analysis of our biochemical data provided new insights into the kinetic properties of the enzyme in particular with respect to oxygen reactivity. A comparative study with the H109R variant demonstrated that the variant suffers from decreased protein stability, cofactor saturation, and substrate affinity. DATABASE: Structural data are available in the PDB database under the accession number 5L46.

-	~~Authors: Hromic~~, A., Pavkov-Keller, T., Gruber, K.	+	Structure and biochemical properties of recombinant human dimethylglycine dehydrogenase and comparison to the disease-related H109R variant.,Augustin P, Hromic A, Pavkov-Keller T, Gruber K, Macheroux P FEBS J. 2016 Aug 3. doi: 10.1111/febs.13828. PMID:27486859<ref>PMID:27486859</ref>

-	~~Description: Crystal structure~~ of ~~human dimethylglycine~~-dehydrogenase	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5l46" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dimethylglycine dehydrogenase]]
		+	[[Category: Gruber, K]]
	[[Category: Hromic, A]]		[[Category: Hromic, A]]
	[[Category: Pavkov-Keller, T]]		[[Category: Pavkov-Keller, T]]
-	[[Category: ~~Gruber, K~~]]	+	[[Category: Covalent flavinylation]]
		+	[[Category: Electron transfer]]
		+	[[Category: One-carbon metabolism]]
		+	[[Category: Oxidoreductase]]

OCA at 13:52, 20 June 2016

OCA — Mon, 20 Jun 2016 13:52:10 GMT

←Older revision		Revision as of 13:52, 20 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5l46 is ON HOLD	+	The entry 5l46 is ON HOLD until Paper Publication

	Authors: Hromic, A., Pavkov-Keller, T., Gruber, K.		Authors: Hromic, A., Pavkov-Keller, T., Gruber, K.

OCA: Protected "5l46" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:29:00 GMT

Protected "5l46" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:29, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5l46 is ON HOLD Authors: Hromic, A., Pavkov-Keller, T., Gruber, K. Description: Crystal structure of human dimethylglycine-dehydrogenase [[Category...

OCA — Wed, 01 Jun 2016 14:28:58 GMT

New page: '''Unreleased structure''' The entry 5l46 is ON HOLD Authors: Hromic, A., Pavkov-Keller, T., Gruber, K. Description: Crystal structure of human dimethylglycine-dehydrogenase [[Category...

New page

'''Unreleased structure'''

The entry 5l46 is ON HOLD

Authors: Hromic, A., Pavkov-Keller, T., Gruber, K.

Description: Crystal structure of human dimethylglycine-dehydrogenase
[[Category: Unreleased Structures]]
[[Category: Hromic, A]]
[[Category: Pavkov-Keller, T]]
[[Category: Gruber, K]]