7pld - Revision history

OCA at 13:06, 1 February 2024

OCA — Thu, 01 Feb 2024 13:06:23 GMT

←Older revision		Revision as of 13:06, 1 February 2024
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	<StructureSection load='7pld' size='340' side='right'caption='[[7pld]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='7pld' size='340' side='right'caption='[[7pld]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7pld]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PLD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pld]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caulobacter_vibrioides_CB15 Caulobacter vibrioides CB15]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PLD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=7UK:(R)~~-~~4-hydroxy-2-pyrrolidone'>7UK</scene>~~, ~~<scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]] 1.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3g4e\|3g4e]], [[4gn7\|4gn7]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7UK:(R)-4-hydroxy-2-pyrrolidone'>7UK</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Xylono-1,4-lactonase Xylono-1,4-lactonase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.68 3.1.1.68]~~ </~~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=7pld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pld OCA], [https://pdbe.org/7pld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pld RCSB], [https://www.ebi.ac.uk/pdbsum/7pld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pld 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=7pld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pld OCA], [https://pdbe.org/7pld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pld RCSB], [https://www.ebi.ac.uk/pdbsum/7pld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pld ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/XYLC_CAUVC XYLC_CAUVC] Involved in the degradation of D-xylose (PubMed:22709678, PubMed:25073011). Catalyzes the hydrolysis of D-xylonolactone to D-xylonate (PubMed:25073011, PubMed:34633186).<ref>PMID:22709678</ref> <ref>PMID:25073011</ref> <ref>PMID:34633186</ref>
	<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: Caulobacter vibrioides CB15]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Xylono-1,4-lactonase]]~~	+	[[Category: Hakulinen N]]
-	[[Category: Hakulinen, N]]	+	[[Category: Paakkonen J]]
-	[[Category: Paakkonen, J]]	+	[[Category: Rouvinen J]]
-	[[Category: Rouvinen, J]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Lactonase]]~~	+
-	~~[[Category: Mononuclear iron]]~~	+
-	~~[[Category: Xylc~~]]	+

OCA at 11:07, 16 February 2022

OCA — Wed, 16 Feb 2022 11:07:12 GMT

←Older revision		Revision as of 11:07, 16 February 2022
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	==Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2-pyrrolidone==		==Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2-pyrrolidone==
-	<StructureSection load='7pld' size='340' side='right'caption='[[7pld]]' scene=''>	+	<StructureSection load='7pld' size='340' side='right'caption='[[7pld]], [[Resolution\|resolution]] 1.70Å' 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=7PLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PLD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7pld]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PLD 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=7pld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pld OCA], [https://pdbe.org/7pld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pld RCSB], [https://www.ebi.ac.uk/pdbsum/7pld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pld 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=7UK:(R)-4-hydroxy-2-pyrrolidone'>7UK</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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;'>[[3g4e\|3g4e]], [[4gn7\|4gn7]]</div></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylono-1,4-lactonase Xylono-1,4-lactonase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.1.68 3.1.1.68] </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=7pld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pld OCA], [https://pdbe.org/7pld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pld RCSB], [https://www.ebi.ac.uk/pdbsum/7pld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pld ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Xylonolactonase Cc XylC from Caulobacter crescentus catalyzes the hydrolysis of the intramolecular ester bond of d-xylonolactone. We have determined crystal structures of Cc XylC in complex with d-xylonolactone isomer analogues d-xylopyranose and (r)-(+)-4-hydroxy-2-pyrrolidinone at high resolution. Cc XylC has a 6-bladed beta-propeller architecture, which contains a central open channel having the active site at one end. According to our previous native mass spectrometry studies, Cc XylC is able to specifically bind Fe(2+) . The crystal structures, presented here, revealed an active site bound metal ion with an octahedral binding geometry. The side chains of three amino acid residues, Glu18, Asn146, and Asp196, which participate in binding of metal ion are located in the same plane. The solved complex structures allowed suggesting a reaction mechanism for intramolecular ester bond hydrolysis in which the major contribution for catalysis arises from the carbonyl oxygen coordination of the xylonolactone substrate to the Fe(2+) . The structure of Cc XylC was compared with eight other ester hydrolases of the beta-propeller hydrolase family. The previously published crystal structures of other beta-propeller hydrolases contain either Ca(2+) , Mg(2+) , or Zn(2+) and show clear similarities in ligand and metal ion binding geometries to that of Cc XylC. It would be interesting to reinvestigate the metal binding specificity of these enzymes and clarify whether they are also able to use Fe(2+) as a catalytic metal. This could further expand our understanding of utilization of Fe(2+) not only in oxidative enzymes but also in hydrolases.
		+
		+	Three-dimensional structure of xylonolactonase from Caulobacter crescentus: A mononuclear iron enzyme of the 6-bladed beta-propeller hydrolase family.,Paakkonen J, Hakulinen N, Andberg M, Koivula A, Rouvinen J Protein Sci. 2021 Nov 11. doi: 10.1002/pro.4229. PMID:34761460<ref>PMID:34761460</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7pld" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hakulinen N]]	+	[[Category: Xylono-1,4-lactonase]]
-	[[Category: Paakkonen J]]	+	[[Category: Hakulinen, N]]
-	[[Category: Rouvinen J]]	+	[[Category: Paakkonen, J]]
		+	[[Category: Rouvinen, J]]
		+	[[Category: Hydrolase]]
		+	[[Category: Lactonase]]
		+	[[Category: Mononuclear iron]]
		+	[[Category: Xylc]]

OCA at 12:37, 24 November 2021

OCA — Wed, 24 Nov 2021 12:37:17 GMT

←Older revision		Revision as of 12:37, 24 November 2021
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-	'''Unreleased structure'''

-	~~The entry 7pld is ON HOLD until Paper Publication~~	+	==Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2-pyrrolidone==
-		+	<StructureSection load='7pld' size='340' side='right'caption='[[7pld]]' scene=''>
-	~~Authors: Paakkonen, J., Hakulinen, N., Rouvinen, J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PLD FirstGlance]. <br>
-	~~Description:~~ Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2-pyrrolidone	+	</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=7pld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pld OCA], [https://pdbe.org/7pld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pld RCSB], [https://www.ebi.ac.uk/pdbsum/7pld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pld ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Rouvinen, J~~]]	+	__TOC__
-	[[Category: Paakkonen, J]]	+	</StructureSection>
-	[[Category: ~~Hakulinen, N~~]]	+	[[Category: Large Structures]]
		+	[[Category: Hakulinen N]]
		+	[[Category: Paakkonen J]]
		+	[[Category: Rouvinen J]]

OCA at 08:10, 15 September 2021

OCA — Wed, 15 Sep 2021 08:10:31 GMT

←Older revision		Revision as of 08:10, 15 September 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Paakkonen, J., Hakulinen, N., Rouvinen, J.		Authors: Paakkonen, J., Hakulinen, N., Rouvinen, J.

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

OCA — Wed, 08 Sep 2021 07:36:24 GMT

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

←Older revision

Revision as of 07:36, 8 September 2021

OCA: New page: '''Unreleased structure''' The entry 7pld is ON HOLD Authors: Paakkonen, J., Hakulinen, N., Rouvinen, J. Description: Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2-pyrrol...

OCA — Wed, 08 Sep 2021 07:36:23 GMT

New page: '''Unreleased structure''' The entry 7pld is ON HOLD Authors: Paakkonen, J., Hakulinen, N., Rouvinen, J. Description: Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2-pyrrol...

New page

'''Unreleased structure'''

The entry 7pld is ON HOLD

Authors: Paakkonen, J., Hakulinen, N., Rouvinen, J.

Description: Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2-pyrrolidone
[[Category: Unreleased Structures]]
[[Category: Rouvinen, J]]
[[Category: Paakkonen, J]]
[[Category: Hakulinen, N]]