7et9 - Revision history

OCA at 10:56, 15 November 2023

OCA — Wed, 15 Nov 2023 10:56:15 GMT

←Older revision		Revision as of 10:56, 15 November 2023
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	<StructureSection load='7et9' size='340' side='right'caption='[[7et9]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='7et9' size='340' side='right'caption='[[7et9]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7et9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ET9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ET9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7et9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ET9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ET9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.9Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-hydroxy-2-oxoheptanedioate_aldolase 4-hydroxy-2-oxoheptanedioate aldolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.52 4.1.2.52] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7et9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7et9 OCA], [https://pdbe.org/7et9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7et9 RCSB], [https://www.ebi.ac.uk/pdbsum/7et9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7et9 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=7et9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7et9 OCA], [https://pdbe.org/7et9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7et9 RCSB], [https://www.ebi.ac.uk/pdbsum/7et9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7et9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A8I1ZEE8_ACIBA A0A8I1ZEE8_ACIBA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7et9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7et9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aldolase 3D structures\|Aldolase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~4-hydroxy-2-oxoheptanedioate aldolase~~]]	+	[[Category: Acinetobacter baumannii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Binlaeh, A]]	+	[[Category: Binlaeh A]]
-	[[Category: Chaiyen, P]]	+	[[Category: Chaiyen P]]
-	[[Category: Chitnumsub, P]]	+	[[Category: Chitnumsub P]]
-	[[Category: Jaruwat, A]]	+	[[Category: Jaruwat A]]
-	[[Category: Maenpuen, S]]	+	[[Category: Maenpuen S]]
-	[[Category: Watthaisong, P]]	+	[[Category: Watthaisong P]]
-	~~[[Category: Aldehyde lyase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 10:56, 16 February 2022

OCA — Wed, 16 Feb 2022 10:56:14 GMT

←Older revision		Revision as of 10:56, 16 February 2022
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	==Crystal structure of AbHpaI-Zn-pyruvate complex, Class II aldolase, HpaI from Acinetobacter baumannii==		==Crystal structure of AbHpaI-Zn-pyruvate complex, Class II aldolase, HpaI from Acinetobacter baumannii==
-	<StructureSection load='7et9' size='340' side='right'caption='[[7et9]]' scene=''>	+	<StructureSection load='7et9' size='340' side='right'caption='[[7et9]], [[Resolution\|resolution]] 1.90Å' 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=7ET9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ET9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7et9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ET9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ET9 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=7et9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7et9 OCA], [https://pdbe.org/7et9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7et9 RCSB], [https://www.ebi.ac.uk/pdbsum/7et9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7et9 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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-hydroxy-2-oxoheptanedioate_aldolase 4-hydroxy-2-oxoheptanedioate aldolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.52 4.1.2.52] </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=7et9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7et9 OCA], [https://pdbe.org/7et9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7et9 RCSB], [https://www.ebi.ac.uk/pdbsum/7et9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7et9 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aldolases catalyze the reversible reactions of aldol condensation and cleavage and have strong potential for the synthesis of chiral compounds, widely used in pharmaceuticals. Here, we investigated a new Class II metal aldolase from the p-hydroxyphenylacetate degradation pathway in Acinetobacter baumannii, 4-hydroxy-2-keto-heptane-1,7-dioate aldolase (AbHpaI), which has various properties suitable for biocatalysis, including stereoselectivity/stereospecificity, broad aldehyde utilization, thermostability, and solvent tolerance. Notably, the use of Zn(2+) by AbHpaI as a native cofactor is distinct from other enzymes in this class. AbHpaI can also use other metal ion (M(2+)) cofactors, except Ca(2+), for catalysis. We found that Zn(2+) yielded the highest enzyme complex thermostability (Tm of 87 degrees C) and solvent tolerance. All AbHpaIM(2+) complexes demonstrated preferential cleavage of (4R)-2-keto-3-deoxy-D-galactonate ((4R)-KDGal) over (4S)-2-keto-3-deoxy-D-gluconate ((4S)-KDGlu), with AbHpaIZn(2+) displaying the highest R/S stereoselectivity ratio (sixfold higher than other M(2+) cofactors). For the aldol condensation reaction, AbHpaIM(2+) only specifically forms (4R)-KDGal and not (4S)-KDGlu and preferentially catalyzes condensation rather than cleavage by approximately 40-fold. Based on 11 X-ray structures of AbHpaI complexed with M(2+) and ligands at 1.85 to 2.0 A resolution, the data clearly indicate that the M(2+) cofactors form an octahedral geometry with Glu151 and Asp177, pyruvate, and water molecules. Moreover, Arg72 in the Zn(2+)-bound form governs the stereoselectivity/stereospecificity of AbHpaI. X-ray structures also show that Ca(2+) binds at the trimer interface via interaction with Asp51. Hence, we conclude that AbHpaIZn(2+) is distinctive from its homologues in substrate stereospecificity, preference for aldol formation over cleavage, and protein robustness, and is attractive for biocatalytic applications.
		+
		+	Catalytic and structural insights into a stereospecific and thermostable Class II aldolase HpaI from Acinetobacter baumannii.,Watthaisong P, Binlaeh A, Jaruwat A, Lawan N, Tantipisit J, Jaroensuk J, Chuaboon L, Phonbuppha J, Tinikul R, Chaiyen P, Chitnumsub P, Maenpuen S J Biol Chem. 2021 Oct 5;297(5):101280. doi: 10.1016/j.jbc.2021.101280. PMID:34624314<ref>PMID:34624314</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7et9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: 4-hydroxy-2-oxoheptanedioate aldolase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Binlaeh A]]	+	[[Category: Binlaeh, A]]
-	[[Category: Chaiyen P]]	+	[[Category: Chaiyen, P]]
-	[[Category: Chitnumsub P]]	+	[[Category: Chitnumsub, P]]
-	[[Category: Jaruwat A]]	+	[[Category: Jaruwat, A]]
-	[[Category: Maenpuen S]]	+	[[Category: Maenpuen, S]]
-	[[Category: Watthaisong P]]	+	[[Category: Watthaisong, P]]
		+	[[Category: Aldehyde lyase]]
		+	[[Category: Lyase]]
		+	[[Category: Tim barrel]]

OCA at 14:29, 3 November 2021

OCA — Wed, 03 Nov 2021 14:29:42 GMT

←Older revision		Revision as of 14:29, 3 November 2021
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-	'''Unreleased structure'''

-	~~The entry 7et9 is ON HOLD until Paper Publication~~	+	==Crystal structure of AbHpaI-Zn-pyruvate complex, Class II aldolase, HpaI from Acinetobacter baumannii==
-		+	<StructureSection load='7et9' size='340' side='right'caption='[[7et9]]' scene=''>
-	~~Authors: Watthaisong, P., Binlaeh, A., Jaruwat, A., Chaiyen, P., Chitnumsub, P., Maenpuen, S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ET9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ET9 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of AbHpaI-Zn-pyruvate complex, Class II aldolase, HpaI from Acinetobacter baumannii	+	</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=7et9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7et9 OCA], [https://pdbe.org/7et9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7et9 RCSB], [https://www.ebi.ac.uk/pdbsum/7et9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7et9 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Binlaeh~~, A]]	+	__TOC__
-	[[Category: ~~Jaruwat,~~ A]]	+	</StructureSection>
-	[[Category: Chaiyen, P]]	+	[[Category: Large Structures]]
-	[[Category: Chitnumsub, P]]	+	[[Category: Binlaeh A]]
-	[[Category: ~~Watthaisong, P~~]]	+	[[Category: Chaiyen P]]
-	[[Category: Maenpuen, S]]	+	[[Category: Chitnumsub P]]
		+	[[Category: Jaruwat A]]
		+	[[Category: Maenpuen S]]
		+	[[Category: Watthaisong P]]

OCA at 06:02, 25 June 2021

OCA — Fri, 25 Jun 2021 06:02:32 GMT

←Older revision		Revision as of 06:02, 25 June 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7et9 is ON HOLD	+	The entry 7et9 is ON HOLD until Paper Publication

	Authors: Watthaisong, P., Binlaeh, A., Jaruwat, A., Chaiyen, P., Chitnumsub, P., Maenpuen, S.		Authors: Watthaisong, P., Binlaeh, A., Jaruwat, A., Chaiyen, P., Chitnumsub, P., Maenpuen, S.

OCA: Protected "7et9" [edit=sysop:move=sysop]

OCA — Wed, 19 May 2021 08:47:28 GMT

Protected "7et9" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:47, 19 May 2021

OCA: New page: '''Unreleased structure''' The entry 7et9 is ON HOLD Authors: Watthaisong, P., Binlaeh, A., Jaruwat, A., Chaiyen, P., Chitnumsub, P., Maenpuen, S. Description: Crystal structure of AbH...

OCA — Wed, 19 May 2021 08:47:26 GMT

New page: '''Unreleased structure''' The entry 7et9 is ON HOLD Authors: Watthaisong, P., Binlaeh, A., Jaruwat, A., Chaiyen, P., Chitnumsub, P., Maenpuen, S. Description: Crystal structure of AbH...

New page

'''Unreleased structure'''

The entry 7et9 is ON HOLD

Authors: Watthaisong, P., Binlaeh, A., Jaruwat, A., Chaiyen, P., Chitnumsub, P., Maenpuen, S.

Description: Crystal structure of AbHpaI-Zn-pyruvate complex, Class II aldolase, HpaI from Acinetobacter baumannii
[[Category: Unreleased Structures]]
[[Category: Binlaeh, A]]
[[Category: Jaruwat, A]]
[[Category: Chaiyen, P]]
[[Category: Chitnumsub, P]]
[[Category: Watthaisong, P]]
[[Category: Maenpuen, S]]