7b2e - Revision history

OCA at 12:20, 1 February 2024

2024-02-01T12:20:56Z

←Older revision		Revision as of 12:20, 1 February 2024
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	<StructureSection load='7b2e' size='340' side='right'caption='[[7b2e]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='7b2e' size='340' side='right'caption='[[7b2e]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7b2e]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Metea Metea~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7B2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7B2E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7b2e]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylorubrum_extorquens_AM1 Methylorubrum extorquens AM1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7B2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7B2E FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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]] 2.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[7ayg\|7ayg]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~MexAM1_META1p0990 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=272630 METEA])</td~~></tr>	+
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Oxalyl-CoA_decarboxylase Oxalyl-CoA decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.8 4.1.1.8]~~ </~~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=7b2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b2e OCA], [https://pdbe.org/7b2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b2e RCSB], [https://www.ebi.ac.uk/pdbsum/7b2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b2e 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=7b2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b2e OCA], [https://pdbe.org/7b2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b2e RCSB], [https://www.ebi.ac.uk/pdbsum/7b2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b2e ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/C5AX46_METEA C5AX46_METEA]
	<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: ~~Metea]]~~	+	[[Category: Methylorubrum extorquens AM1]]
-	~~[[Category: Oxalyl-CoA decarboxylase~~]]	+	[[Category: Burgener S]]
-	[[Category: Burgener, S]]	+	[[Category: Erb TJ]]
-	[[Category: Erb~~, T J~~]]	+	[[Category: Nattermann M]]
-	[[Category: Nattermann, M]]	+	[[Category: Pfister P]]
-	[[Category: Pfister, P]]	+	[[Category: Zarzycki J]]
-	[[Category: Zarzycki, J]]	+
-	~~[[Category: Carboxylase]]~~	+
-	~~[[Category: Decarboxylase]]~~	+
-	~~[[Category: Formyl-coa]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Mandelyl-coa]]~~	+
-	~~[[Category: Oxalyl-coa~~]]	+

OCA at 12:48, 13 October 2021

2021-10-13T12:48:46Z

←Older revision		Revision as of 12:48, 13 October 2021
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	==quadruple mutant of oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP and ADP==		==quadruple mutant of oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP and ADP==
-	<StructureSection load='7b2e' size='340' side='right'caption='[[7b2e]]' scene=''>	+	<StructureSection load='7b2e' size='340' side='right'caption='[[7b2e]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7B2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7B2E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7b2e]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Metea Metea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7B2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7B2E FirstGlance]. <br>
-	</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=7b2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b2e OCA], [https://pdbe.org/7b2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b2e RCSB], [https://www.ebi.ac.uk/pdbsum/7b2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b2e ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7ayg\|7ayg]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MexAM1_META1p0990 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272630 METEA])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Oxalyl-CoA_decarboxylase Oxalyl-CoA decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.8 4.1.1.8] </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=7b2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b2e OCA], [https://pdbe.org/7b2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b2e RCSB], [https://www.ebi.ac.uk/pdbsum/7b2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b2e ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	One of the biggest challenges to realize a circular carbon economy is the synthesis of complex carbon compounds from one-carbon (C1) building blocks. Since the natural solution space of C1-C1 condensations is limited to highly complex enzymes, the development of more simple and robust biocatalysts may facilitate the engineering of C1 assimilation routes. Thiamine diphosphate-dependent enzymes harbor great potential for this task, due to their ability to create C-C bonds. Here, we employed structure-guided iterative saturation mutagenesis to convert oxalyl-CoA decarboxylase (OXC) from Methylobacterium extorquens into a glycolyl-CoA synthase (GCS) that allows for the direct condensation of the two C1 units formyl-CoA and formaldehyde. A quadruple variant MeOXC4 showed a 100000-fold switch between OXC and GCS activities, a 200-fold increase in the GCS activity compared to the wild type, and formaldehyde affinity that is comparable to natural formaldehyde-converting enzymes. Notably, MeOCX4 outcompetes all other natural and engineered enzymes for C1-C1 condensations by more than 40-fold in catalytic efficiency and is highly soluble in Escherichia coli. In addition to the increased GCS activity, MeOXC4 showed up to 300-fold higher activity than the wild type toward a broad range of carbonyl acceptor substrates. When applied in vivo, MeOXC4 enables the production of glycolate from formaldehyde, overcoming the current bottleneck of C1-C1 condensation in whole-cell bioconversions and paving the way toward synthetic C1 assimilation routes in vivo.
		+
		+	Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism.,Nattermann M, Burgener S, Pfister P, Chou A, Schulz L, Lee SH, Paczia N, Zarzycki J, Gonzalez R, Erb TJ ACS Catal. 2021 May 7;11(9):5396-5404. doi: 10.1021/acscatal.1c01237. Epub 2021, Apr 20. PMID:34484855<ref>PMID:34484855</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7b2e" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Burgener S]]	+	[[Category: Metea]]
-	[[Category: Erb TJ]]	+	[[Category: Oxalyl-CoA decarboxylase]]
-	[[Category: Nattermann M]]	+	[[Category: Burgener, S]]
-	[[Category: Pfister P]]	+	[[Category: Erb, T J]]
-	[[Category: Zarzycki J]]	+	[[Category: Nattermann, M]]
		+	[[Category: Pfister, P]]
		+	[[Category: Zarzycki, J]]
		+	[[Category: Carboxylase]]
		+	[[Category: Decarboxylase]]
		+	[[Category: Formyl-coa]]
		+	[[Category: Ligase]]
		+	[[Category: Lyase]]
		+	[[Category: Mandelyl-coa]]
		+	[[Category: Oxalyl-coa]]

OCA at 05:19, 28 April 2021

2021-04-28T05:19:19Z

←Older revision		Revision as of 05:19, 28 April 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7b2e ~~is ON HOLD until Paper Publication~~	+	==quadruple mutant of oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP and ADP==
-		+	<StructureSection load='7b2e' size='340' side='right'caption='[[7b2e]]' scene=''>
-	~~Authors~~: ~~Pfister~~, P., ~~Burgener, S~~., ~~Nattermann, M~~.~~, Zarzycki, J~~., ~~Erb~~, T.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7B2E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7B2E FirstGlance]. <br>
-	~~Description: quadruple mutant of oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP and ADP~~	+	</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=7b2e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7b2e OCA], [https://pdbe.org/7b2e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7b2e RCSB], [https://www.ebi.ac.uk/pdbsum/7b2e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7b2e ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Pfister, P~~]]	+	__TOC__
-	[[Category: Erb~~, T.J~~]]	+	</StructureSection>
-	[[Category: ~~Zarzycki, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Nattermann, M~~]]	+	[[Category: Burgener S]]
-	[[Category: ~~Burgener, S~~]]	+	[[Category: Erb TJ]]
		+	[[Category: Nattermann M]]
		+	[[Category: Pfister P]]
		+	[[Category: Zarzycki J]]

OCA at 05:13, 30 December 2020

2020-12-30T05:13:00Z

←Older revision		Revision as of 05:13, 30 December 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7b2e is ON HOLD	+	The entry 7b2e is ON HOLD until Paper Publication

	Authors: Pfister, P., Burgener, S., Nattermann, M., Zarzycki, J., Erb, T.J.		Authors: Pfister, P., Burgener, S., Nattermann, M., Zarzycki, J., Erb, T.J.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Pfister, P]]		[[Category: Pfister, P]]
-	[[Category: Nattermann, M]]
	[[Category: Erb, T.J]]		[[Category: Erb, T.J]]
	[[Category: Zarzycki, J]]		[[Category: Zarzycki, J]]
		+	[[Category: Nattermann, M]]
	[[Category: Burgener, S]]		[[Category: Burgener, S]]

OCA: Protected "7b2e" [edit=sysop:move=sysop]

2020-12-02T05:37:06Z

Protected "7b2e" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:37, 2 December 2020

OCA: New page: '''Unreleased structure''' The entry 7b2e is ON HOLD Authors: Pfister, P., Burgener, S., Nattermann, M., Zarzycki, J., Erb, T.J. Description: quadruple mutant of oxalyl-CoA decarboxyla...

2020-12-02T05:37:05Z

New page: '''Unreleased structure''' The entry 7b2e is ON HOLD Authors: Pfister, P., Burgener, S., Nattermann, M., Zarzycki, J., Erb, T.J. Description: quadruple mutant of oxalyl-CoA decarboxyla...

New page

'''Unreleased structure'''

The entry 7b2e is ON HOLD

Authors: Pfister, P., Burgener, S., Nattermann, M., Zarzycki, J., Erb, T.J.

Description: quadruple mutant of oxalyl-CoA decarboxylase from Methylorubrum extorquens with bound TPP and ADP
[[Category: Unreleased Structures]]
[[Category: Pfister, P]]
[[Category: Nattermann, M]]
[[Category: Erb, T.J]]
[[Category: Zarzycki, J]]
[[Category: Burgener, S]]