4xye - Revision history

OCA at 10:51, 10 January 2024

2024-01-10T10:51:25Z

←Older revision		Revision as of 10:51, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xye]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Granulicella_mallensis_MP5ACTX8 Granulicella mallensis MP5ACTX8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XYE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xye]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Granulicella_mallensis_MP5ACTX8 Granulicella mallensis MP5ACTX8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XYE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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=4xye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xye OCA], [https://pdbe.org/4xye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xye RCSB], [https://www.ebi.ac.uk/pdbsum/4xye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xye 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=4xye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xye OCA], [https://pdbe.org/4xye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xye RCSB], [https://www.ebi.ac.uk/pdbsum/4xye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xye ProSAT]</span></td></tr>
	</table>		</table>

OCA at 17:58, 26 April 2023

2023-04-26T17:58:23Z

←Older revision		Revision as of 17:58, 26 April 2023
Line 1:		Line 1:

	==GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+)==		==GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+)==
-	<StructureSection load='4xye' size='340' side='right' caption='[[4xye]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='4xye' size='340' side='right'caption='[[4xye]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xye]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Acidobacterium_sp._mp5actx8 Acidobacterium sp. mp5actx8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XYE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xye]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Granulicella_mallensis_MP5ACTX8 Granulicella mallensis MP5ACTX8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XYE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xyb\|4xyb]], [[4xyg\|4xyg]]</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=4xye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xye OCA], [https://pdbe.org/4xye PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xye RCSB], [https://www.ebi.ac.uk/pdbsum/4xye PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xye ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AciX8_2172 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=682795 Acidobacterium sp. MP5ACTX8])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </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=4xye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xye OCA], [~~http~~://pdbe.org/4xye PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xye RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xye PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xye ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G8NVB5_GRAMM G8NVB5_GRAMM]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4xye" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4xye" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Formate dehydrogenase 3D structures\|Formate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Acidobacterium sp. mp5actx8~~]]	+	[[Category: Granulicella mallensis MP5ACTX8]]
-	[[Category: ~~Formate dehydrogenase~~]]	+	[[Category: Large Structures]]
-	[[Category: Beneventi, E]]	+	[[Category: Beneventi E]]
-	[[Category: Bergantino, E]]	+	[[Category: Bergantino E]]
-	[[Category: Cendron, L]]	+	[[Category: Cendron L]]
-	[[Category: Fogal, S]]	+	[[Category: Fogal S]]
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 14:28, 16 November 2017

2017-11-16T14:28:45Z

←Older revision		Revision as of 14:28, 16 November 2017
Line 1:		Line 1:
		+
	==GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+)==		==GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+)==
	<StructureSection load='4xye' size='340' side='right' caption='[[4xye]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4xye' size='340' side='right' caption='[[4xye]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xye]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XYE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xye]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Acidobacterium_sp._mp5actx8 Acidobacterium sp. mp5actx8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XYE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xyb\|4xyb]], [[4xyg\|4xyg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xyb\|4xyb]], [[4xyg\|4xyg]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AciX8_2172 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=682795 Acidobacterium sp. MP5ACTX8])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </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=4xye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xye OCA], [http://pdbe.org/4xye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xye RCSB], [http://www.ebi.ac.uk/pdbsum/4xye PDBsum]</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=4xye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xye OCA], [http://pdbe.org/4xye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xye RCSB], [http://www.ebi.ac.uk/pdbsum/4xye PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xye ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Acidobacterium sp. mp5actx8]]
	[[Category: Formate dehydrogenase]]		[[Category: Formate dehydrogenase]]
	[[Category: Beneventi, E]]		[[Category: Beneventi, E]]

OCA at 21:52, 30 November 2015

2015-11-30T21:52:02Z

←Older revision		Revision as of 21:52, 30 November 2015
Line 6:		Line 6:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xyb\|4xyb]], [[4xyg\|4xyg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xyb\|4xyb]], [[4xyg\|4xyg]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </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=4xye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xye OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xye RCSB], [http://www.ebi.ac.uk/pdbsum/4xye PDBsum]</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=4xye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xye OCA], [http://pdbe.org/4xye PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xye RCSB], [http://www.ebi.ac.uk/pdbsum/4xye PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4xye" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:45, 8 July 2015

2015-07-08T14:45:09Z

←Older revision		Revision as of 14:45, 8 July 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+)==
		+	<StructureSection load='4xye' size='340' side='right' caption='[[4xye]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xye]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XYE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XYE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4xyb\|4xyb]], [[4xyg\|4xyg]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Formate_dehydrogenase Formate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.2 1.2.1.2] </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=4xye FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xye OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xye RCSB], [http://www.ebi.ac.uk/pdbsum/4xye PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Formate dehydrogenases (FDHs) are considered particularly useful enzymes in biocatalysis when the regeneration of the cofactor NAD(P)H is required, that is, in chiral synthesis with dehydrogenases. Their utilization is however limited to the recycling of NAD+, since all (apart one) of the FDHs characterized so far are strictly specific for this cofactor, and this is a major drawback for their otherwise wide applicability. Despite the many attempts performed to modify cofactor specificity by protein engineering different NAD+-dependent FDHs, in the general practice, glucose or phosphite dehydrogenases are chosen for the recycling of NADP+. We report on the functional and structural characterization of a new FDH, GraFDH, identified by mining the genome of the extremophile prokaryote Granulicella mallensis MP5ACTX8. The new enzyme displays a valuable stability in the presence of many organic cosolvents as well as double cofactor specificity, with NADP+ preferred over NAD+ at acidic pH values, at which it also shows the highest stability. The quite low affinities for both cofactors as well as for the substrate formate indicate, however, that the native enzyme requires optimization to be applied as biocatalytic tool. We also determined the crystal structure of GraFDH both as apoprotein and as holoprotein, either in complex with NAD+ or NADP+. Noticeably, the latter represents the first structure of an FDH enzyme in complex with NADP+. This fine picture of the structural determinants involved in cofactor selectivity will possibly boost protein engineering of the new enzyme or other homolog FDHs in view of their biocatalytic exploitation for NADP+ recycling.

-	~~The entry 4xye is ON HOLD until Paper Publication~~	+	Structural basis for double cofactor specificity in a new formate dehydrogenase from the acidobacterium Granulicella mallensis MP5ACTX8.,Fogal S, Beneventi E, Cendron L, Bergantino E Appl Microbiol Biotechnol. 2015 Jun 24. PMID:26104866<ref>PMID:26104866</ref>

-	~~Authors: Cendron~~, L.~~, Fogal,~~ S.~~, Beneventi, E., Bergantino, E~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+)~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Formate dehydrogenase]]
		+	[[Category: Beneventi, E]]
	[[Category: Bergantino, E]]		[[Category: Bergantino, E]]
-	[[Category: Beneventi, E]]
	[[Category: Cendron, L]]		[[Category: Cendron, L]]
	[[Category: Fogal, S]]		[[Category: Fogal, S]]
		+	[[Category: Nad]]
		+	[[Category: Oxidoreductase]]

OCA: Protected "4xye" [edit=sysop:move=sysop]

2015-02-12T10:51:52Z

Protected "4xye" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:51, 12 February 2015

OCA: New page: '''Unreleased structure''' The entry 4xye is ON HOLD until Paper Publication Authors: Cendron, L., Fogal, S., Beneventi, E., Bergantino, E. Description: GRANULICELLA M. FORMATE DEHYDRO...

2015-02-12T10:51:50Z

New page: '''Unreleased structure''' The entry 4xye is ON HOLD until Paper Publication Authors: Cendron, L., Fogal, S., Beneventi, E., Bergantino, E. Description: GRANULICELLA M. FORMATE DEHYDRO...

New page

'''Unreleased structure'''

The entry 4xye is ON HOLD until Paper Publication

Authors: Cendron, L., Fogal, S., Beneventi, E., Bergantino, E.

Description: GRANULICELLA M. FORMATE DEHYDROGENASE (FDH) IN COMPLEX WITH NAD(+)
[[Category: Unreleased Structures]]
[[Category: Bergantino, E]]
[[Category: Beneventi, E]]
[[Category: Cendron, L]]
[[Category: Fogal, S]]