4xdz - Revision history

OCA at 07:44, 27 September 2023

OCA — Wed, 27 Sep 2023 07:44:32 GMT

←Older revision		Revision as of 07:44, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4xdz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ignisphaera_aggregans_DSM_17230 Ignisphaera aggregans DSM 17230]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XDZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[4xdz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ignisphaera_aggregans_DSM_17230 Ignisphaera aggregans DSM 17230]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XDZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=40E:OXO(PROPAN-2-YLAMINO)ACETIC+ACID'>40E</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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]] 1.15Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=40E:OXO(PROPAN-2-YLAMINO)ACETIC+ACID'>40E</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=4xdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xdz OCA], [https://pdbe.org/4xdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xdz RCSB], [https://www.ebi.ac.uk/pdbsum/4xdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xdz 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=4xdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xdz OCA], [https://pdbe.org/4xdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xdz RCSB], [https://www.ebi.ac.uk/pdbsum/4xdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xdz ProSAT]</span></td></tr>
	</table>		</table>

OCA at 21:24, 12 April 2023

OCA — Wed, 12 Apr 2023 21:24:51 GMT

←Older revision		Revision as of 21:24, 12 April 2023
Line 3:		Line 3:
	<StructureSection load='4xdz' size='340' side='right'caption='[[4xdz]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='4xdz' size='340' side='right'caption='[[4xdz]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xdz]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ignaa Ignaa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XDZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4XDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xdz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ignisphaera_aggregans_DSM_17230 Ignisphaera aggregans DSM 17230]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XDZ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=40E:OXO(PROPAN-2-YLAMINO)ACETIC+ACID'>40E</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=40E:OXO(PROPAN-2-YLAMINO)ACETIC+ACID'>40E</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ilvC, Igag_1561 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=583356 IGNAA])</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=4xdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xdz OCA], [https://pdbe.org/4xdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xdz RCSB], [https://www.ebi.ac.uk/pdbsum/4xdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xdz ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ketol-acid_reductoisomerase Ketol-acid reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.86 1.1.1.86] </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=4xdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xdz OCA], [~~http~~://pdbe.org/4xdz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4xdz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4xdz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4xdz ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/ILVC_IGNAA ILVC_IGNAA] Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol-acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3-dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3-hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH or NADH to yield (R)-2,3-dihydroxy-isovalerate.<ref>PMID:25172159</ref> <ref>PMID:26644020</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Ketol-acid reductoisomerase\|Ketol-acid reductoisomerase]]	+	*[[Ketol-acid reductoisomerase 3D structures\|Ketol-acid reductoisomerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ignaa]]~~	+	[[Category: Ignisphaera aggregans DSM 17230]]
-	~~[[Category: Ketol-acid reductoisomerase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arnold~~, F H~~]]	+	[[Category: Arnold FH]]
-	[[Category: Brinkmann-Chen, S]]	+	[[Category: Brinkmann-Chen S]]
-	[[Category: Cahn~~, J K.B]]~~	+	[[Category: Cahn JKB]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 07:42, 29 May 2019

OCA — Wed, 29 May 2019 07:42:52 GMT

←Older revision		Revision as of 07:42, 29 May 2019
Line 1:		Line 1:
		+
	==Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans==		==Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans==
-	<StructureSection load='4xdz' size='340' side='right' caption='[[4xdz]], [[Resolution\|resolution]] 1.15Å' scene=''>	+	<StructureSection load='4xdz' size='340' side='right'caption='[[4xdz]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4xdz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4xdz]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ignaa Ignaa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XDZ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=40E:OXO(PROPAN-2-YLAMINO)ACETIC+ACID'>40E</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=40E:OXO(PROPAN-2-YLAMINO)ACETIC+ACID'>40E</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ilvC, Igag_1561 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=583356 IGNAA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ketol-acid_reductoisomerase Ketol-acid reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.86 1.1.1.86] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ketol-acid_reductoisomerase Ketol-acid reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.86 1.1.1.86] </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=4xdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xdz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xdz RCSB], [http://www.ebi.ac.uk/pdbsum/4xdz 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=4xdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xdz OCA], [http://pdbe.org/4xdz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4xdz RCSB], [http://www.ebi.ac.uk/pdbsum/4xdz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4xdz ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 17:
	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 4xdz" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 22:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ignaa]]
	[[Category: Ketol-acid reductoisomerase]]		[[Category: Ketol-acid reductoisomerase]]
		+	[[Category: Large Structures]]
	[[Category: Arnold, F H]]		[[Category: Arnold, F H]]
	[[Category: Brinkmann-Chen, S]]		[[Category: Brinkmann-Chen, S]]

OCA at 05:04, 9 September 2015

OCA — Wed, 09 Sep 2015 05:04:30 GMT

←Older revision		Revision as of 05:04, 9 September 2015
Line 15:		Line 15:
	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>
		+
		+	==See Also==
		+	*[[Ketol-acid reductoisomerase\|Ketol-acid reductoisomerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:48, 22 April 2015

OCA — Wed, 22 Apr 2015 12:48:35 GMT

←Older revision		Revision as of 12:48, 22 April 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans==
		+	<StructureSection load='4xdz' size='340' side='right' caption='[[4xdz]], [[Resolution\|resolution]] 1.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4xdz]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4XDZ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=40E:OXO(PROPAN-2-YLAMINO)ACETIC+ACID'>40E</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ketol-acid_reductoisomerase Ketol-acid reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.86 1.1.1.86] </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=4xdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xdz OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4xdz RCSB], [http://www.ebi.ac.uk/pdbsum/4xdz PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Although most sequenced members of the industrially important ketol-acid reductoisomerase (KARI) family are Class I enzymes, structural studies to date have focused primarily on the Class II KARIs, which arose through domain duplication. Here, we present five new crystal structures of Class I KARIs. These include the first structure of a KARI with a 6-residue beta2alphaB (cofactor specificity determining) loop and an NADPH phosphate binding geometry distinct from that of the 7- and 12-residue loops. We also present the first structures of naturally occurring KARIs that utilize NADH as cofactor. These results show insertions in the specificity loops that confounded previous attempts to classify them according to loop length. Lastly, we explore the conformational changes that occur in Class I KARIs upon binding of cofactor and metal ions. The Class I KARI structures indicate that the active sites close upon binding NAD(P)H, similar to what is observed in the Class II KARIs of rice and spinach and different from the opening of the active site observed in the Class II KARI of E. coli. This conformational change involves a decrease in the bending of the helix that runs between the domains and a rearrangement of the nicotinamide binding site.

-	~~The entry 4xdz is ON HOLD until Paper Publication~~	+	Cofactor specificity motifs and the induced fit mechanism in Class I ketol-acid reductoisomerases.,Cahn JK, Brinkmann-Chen S, Spatzal T, Wiig JA, Buller AR, Einsle O, Hu Y, Ribbe MW, Arnold FH Biochem J. 2015 Apr 7. PMID:25849365<ref>PMID:25849365</ref>

-	~~Authors: Cahn~~, ~~J.K~~.~~B., Brinkmann-Chen,~~ S.~~, Arnold, F.H~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Holo structure of ketol~~-acid reductoisomerase ~~from Ignisphaera aggregans~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ketol-acid reductoisomerase]]
		+	[[Category: Arnold, F H]]
	[[Category: Brinkmann-Chen, S]]		[[Category: Brinkmann-Chen, S]]
-	[[Category: Cahn, J.K.B]]	+	[[Category: Cahn, J K.B]]
-	[[Category: ~~Arnold, F.H~~]]	+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]

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

OCA — Wed, 31 Dec 2014 14:02:25 GMT

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

←Older revision

Revision as of 14:02, 31 December 2014

OCA: New page: '''Unreleased structure''' The entry 4xdz is ON HOLD until Paper Publication Authors: Cahn, J.K.B., Brinkmann-Chen, S., Arnold, F.H. Description: Holo structure of ketol-acid reductois...

OCA — Wed, 31 Dec 2014 14:02:23 GMT

New page: '''Unreleased structure''' The entry 4xdz is ON HOLD until Paper Publication Authors: Cahn, J.K.B., Brinkmann-Chen, S., Arnold, F.H. Description: Holo structure of ketol-acid reductois...

New page

'''Unreleased structure'''

The entry 4xdz is ON HOLD until Paper Publication

Authors: Cahn, J.K.B., Brinkmann-Chen, S., Arnold, F.H.

Description: Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans
[[Category: Unreleased Structures]]
[[Category: Brinkmann-Chen, S]]
[[Category: Cahn, J.K.B]]
[[Category: Arnold, F.H]]