4j1o - Revision history

OCA at 12:00, 1 March 2024

OCA — Fri, 01 Mar 2024 12:00:30 GMT

←Older revision		Revision as of 12:00, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans_PD1222 Paracoccus denitrificans PD1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J1O FirstGlance]. <br>		<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans_PD1222 Paracoccus denitrificans PD1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J1O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PBE:1,1-DIMETHYL-PROLINIUM'>PBE</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]] 1.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PBE:1,1-DIMETHYL-PROLINIUM'>PBE</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=4j1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j1o OCA], [https://pdbe.org/4j1o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j1o RCSB], [https://www.ebi.ac.uk/pdbsum/4j1o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j1o 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=4j1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j1o OCA], [https://pdbe.org/4j1o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j1o RCSB], [https://www.ebi.ac.uk/pdbsum/4j1o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j1o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/HPBD_PARDP HPBD_PARDP] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>		[https://www.uniprot.org/uniprot/HPBD_PARDP HPBD_PARDP] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	UNLABELLED: Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. IMPORTANCE: At least half of the extant protein annotations are incorrect, and the errors propagate as the number of genome sequences increases exponentially. A large-scale, multidisciplinary sequence- and structure-based strategy for functional assignment of bacterial enzymes of unknown function has demonstrated the pathway for catabolism of the osmoprotectant proline betaine.
-
-	Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.,Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE MBio. 2014 Feb 11;5(1):e00933-13. doi: 10.1128/mBio.00933-13. PMID:24520058<ref>PMID:24520058</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4j1o" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 21:24, 16 November 2022

OCA — Wed, 16 Nov 2022 21:24:16 GMT

←Older revision		Revision as of 21:24, 16 November 2022
Line 3:		Line 3:
	<StructureSection load='4j1o' size='340' side='right'caption='[[4j1o]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4j1o' size='340' side='right'caption='[[4j1o]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pardp Pardp~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4J1O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans_PD1222 Paracoccus denitrificans PD1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4J1O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PBE:1,1-DIMETHYL-PROLINIUM'>PBE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PBE:1,1-DIMETHYL-PROLINIUM'>PBE</scene></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=4j1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j1o OCA], [~~http~~://pdbe.org/4j1o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4j1o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4j1o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4j1o 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=4j1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j1o OCA], [https://pdbe.org/4j1o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4j1o RCSB], [https://www.ebi.ac.uk/pdbsum/4j1o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4j1o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HPBD_PARDP HPBD_PARDP]] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>	+	[https://www.uniprot.org/uniprot/HPBD_PARDP HPBD_PARDP] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pardp~~]]	+	[[Category: Paracoccus denitrificans PD1222]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Almo SC]]
-	[[Category: Bhosle, R]]	+	[[Category: Bhosle R]]
-	[[Category: Bonanno~~, J B~~]]	+	[[Category: Bonanno JB]]
-	[[Category: Chamala, S]]	+	[[Category: Chamala S]]
-	[[Category: Evans, B]]	+	[[Category: Evans B]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Gizzi, A]]	+	[[Category: Gizzi A]]
-	[[Category: Hammonds, J]]	+	[[Category: Hammonds J]]
-	[[Category: Hillerich, B]]	+	[[Category: Hillerich B]]
-	[[Category: Kar, A]]	+	[[Category: Kar A]]
-	[[Category: LaFleur, J]]	+	[[Category: LaFleur J]]
-	[[Category: Love, J]]	+	[[Category: Love J]]
-	[[Category: Morisco~~, L L]]~~	+	[[Category: Morisco LL]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Seidel RD]]
-	[[Category: Seidel~~, R D~~]]	+	[[Category: Sojitra S]]
-	[[Category: Sojitra, S]]	+	[[Category: Stead M]]
-	[[Category: Stead, M]]	+	[[Category: Toro R]]
-	[[Category: Toro, R]]	+	[[Category: Vetting MW]]
-	[[Category: Vetting~~, M W~~]]	+	[[Category: Villigas G]]
-	[[Category: Villigas, G]]	+	[[Category: Wasserman SR]]
-	[[Category: Wasserman~~, S R]]~~	+
-	~~[[Category: Betaine racemase]]~~	+
-	~~[[Category: Enolase]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Nysgrc]]~~	+
-	~~[[Category: Proline betaine racemease]]~~	+
-	~~[[Category: Psi-biology~~]]	+

OCA at 05:17, 13 February 2020

OCA — Thu, 13 Feb 2020 05:17:44 GMT

←Older revision		Revision as of 05:17, 13 February 2020
Line 1:		Line 1:

	==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)==		==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)==
-	<StructureSection load='4j1o' size='340' side='right' caption='[[4j1o]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='4j1o' size='340' side='right'caption='[[4j1o]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J1O FirstGlance]. <br>		<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J1O FirstGlance]. <br>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4j1o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4j1o" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Mandelate racemase/muconate lactonizing enzyme 3D structures\|Mandelate racemase/muconate lactonizing enzyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pardp]]		[[Category: Pardp]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]

OCA at 20:04, 24 January 2018

OCA — Wed, 24 Jan 2018 20:04:01 GMT

←Older revision		Revision as of 20:04, 24 January 2018
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/HPBD_PARDP HPBD_PARDP]] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>		[[http://www.uniprot.org/uniprot/HPBD_PARDP HPBD_PARDP]] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	UNLABELLED: Through the use of genetic, enzymatic, metabolomic, and structural analyses, we have discovered the catabolic pathway for proline betaine, an osmoprotectant, in Paracoccus denitrificans and Rhodobacter sphaeroides. Genetic and enzymatic analyses showed that several of the key enzymes of the hydroxyproline betaine degradation pathway also function in proline betaine degradation. Metabolomic analyses detected each of the metabolic intermediates of the pathway. The proline betaine catabolic pathway was repressed by osmotic stress and cold stress, and a regulatory transcription factor was identified. We also report crystal structure complexes of the P. denitrificans HpbD hydroxyproline betaine epimerase/proline betaine racemase with l-proline betaine and cis-hydroxyproline betaine. IMPORTANCE: At least half of the extant protein annotations are incorrect, and the errors propagate as the number of genome sequences increases exponentially. A large-scale, multidisciplinary sequence- and structure-based strategy for functional assignment of bacterial enzymes of unknown function has demonstrated the pathway for catabolism of the osmoprotectant proline betaine.
		+
		+	Prediction and biochemical demonstration of a catabolic pathway for the osmoprotectant proline betaine.,Kumar R, Zhao S, Vetting MW, Wood BM, Sakai A, Cho K, Solbiati J, Almo SC, Sweedler JV, Jacobson MP, Gerlt JA, Cronan JE MBio. 2014 Feb 11;5(1):e00933-13. doi: 10.1128/mBio.00933-13. PMID:24520058<ref>PMID:24520058</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4j1o" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:27, 11 August 2016

OCA — Thu, 11 Aug 2016 09:27:49 GMT

←Older revision		Revision as of 09:27, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)==		==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)==
	<StructureSection load='4j1o' size='340' side='right' caption='[[4j1o]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='4j1o' size='340' side='right' caption='[[4j1o]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J1O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pardp Pardp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J1O FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PBE:1,1-DIMETHYL-PROLINIUM'>PBE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PBE:1,1-DIMETHYL-PROLINIUM'>PBE</scene></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=4j1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j1o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4j1o RCSB], [http://www.ebi.ac.uk/pdbsum/4j1o 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=4j1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j1o OCA], [http://pdbe.org/4j1o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4j1o RCSB], [http://www.ebi.ac.uk/pdbsum/4j1o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4j1o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~A1B198_PARDP A1B198_PARDP~~]] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>	+	[[http://www.uniprot.org/uniprot/HPBD_PARDP HPBD_PARDP]] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Paracoccus denitrificans pd1222~~]]	+	[[Category: Pardp]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Bhosle, R]]		[[Category: Bhosle, R]]

OCA at 12:58, 4 January 2015

OCA — Sun, 04 Jan 2015 12:58:16 GMT

←Older revision		Revision as of 12:58, 4 January 2015
Line 1:		Line 1:
-	~~[[Image:4j1o.jpg\|left\|200px]]~~	+	==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)==
-		+	<StructureSection load='4j1o' size='340' side='right' caption='[[4j1o]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{STRUCTURE_4j1o\| PDB=4j1o \| SCENE= }}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4j1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4J1O FirstGlance]. <br>
-	===Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)===	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PBE:1,1-DIMETHYL-PROLINIUM'>PBE</scene></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=4j1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4j1o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4j1o RCSB], [http://www.ebi.ac.uk/pdbsum/4j1o PDBsum]</span></td></tr>
-		+	</table>
-	==~~About this Structure~~==	+	== Function ==
-	[[4j1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA].	+	[[http://www.uniprot.org/uniprot/A1B198_PARDP A1B198_PARDP]] Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. Can also catalyze the racemization of L-proline betaine.<ref>PMID:24056934</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Paracoccus denitrificans pd1222]]		[[Category: Paracoccus denitrificans pd1222]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Bhosle, R.]]	+	[[Category: Bhosle, R]]
-	[[Category: Bonanno, J B.]]	+	[[Category: Bonanno, J B]]
-	[[Category: Chamala, S.]]	+	[[Category: Chamala, S]]
-	[[Category: Evans, B.]]	+	[[Category: Evans, B]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Gizzi, A.]]	+	[[Category: Gizzi, A]]
-	[[Category: Hammonds, J.]]	+	[[Category: Hammonds, J]]
-	[[Category: Hillerich, B.]]	+	[[Category: Hillerich, B]]
-	[[Category: Kar, A.]]	+	[[Category: Kar, A]]
-	[[Category: LaFleur, J.]]	+	[[Category: LaFleur, J]]
-	[[Category: Love, J.]]	+	[[Category: Love, J]]
-	[[Category: Morisco, L L.]]	+	[[Category: Morisco, L L]]
-	[[Category: ~~NYSGRC, New York~~ Structural ~~Genomics Research Consortium.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Seidel, R D.]]	+	[[Category: Seidel, R D]]
-	[[Category: Sojitra, S.]]	+	[[Category: Sojitra, S]]
-	[[Category: Stead, M.]]	+	[[Category: Stead, M]]
-	[[Category: Toro, R.]]	+	[[Category: Toro, R]]
-	[[Category: Vetting, M W.]]	+	[[Category: Vetting, M W]]
-	[[Category: Villigas, G.]]	+	[[Category: Villigas, G]]
-	[[Category: Wasserman, S R.]]	+	[[Category: Wasserman, S R]]
	[[Category: Betaine racemase]]		[[Category: Betaine racemase]]
	[[Category: Enolase]]		[[Category: Enolase]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
-	[[Category: New york structural genomics research consortium]]
	[[Category: Nysgrc]]		[[Category: Nysgrc]]
	[[Category: Proline betaine racemease]]		[[Category: Proline betaine racemease]]
	[[Category: Psi-biology]]		[[Category: Psi-biology]]
-	[[Category: Structural genomic]]

OCA at 14:30, 6 March 2013

OCA — Wed, 06 Mar 2013 14:30:50 GMT

←Older revision		Revision as of 14:30, 6 March 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4j1o.jpg\|left\|200px]]

-	~~The entry~~ 4j1o ~~is ON HOLD~~	+	{{STRUCTURE_4j1o\| PDB=4j1o \| SCENE= }}

-	Authors: Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala,S., Kar, A., LaFleur, J., Villigas, G., Evans, B., Hammonds, J., Gizzi, A., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Bonanno, J.B., Gerlt, J.A., Almo, S.C., New York Structural Genomics Research Consortium (~~NYSGRC~~)	+	===Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound l-proline betaine (substrate)===

-	~~Description~~: ~~CRYSTAL STRUCTURE OF AN ENOLASE (MANDELATE RACEMASE SUBGROUP) FROM PARACOCOCUS DENITRIFICANS PD1222 (TARGET NYSGRC~~-~~012907) WITH BOUND~~ L-~~PROLINE BETAINE (SUBSTRATE)~~	+
		+	==About this Structure==
		+	[[4j1o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans_pd1222 Paracoccus denitrificans pd1222]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4J1O OCA].
		+	[[Category: Paracoccus denitrificans pd1222]]
		+	[[Category: Almo, S C.]]
		+	[[Category: Bhosle, R.]]
		+	[[Category: Bonanno, J B.]]
		+	[[Category: Chamala, S.]]
		+	[[Category: Evans, B.]]
		+	[[Category: Gerlt, J A.]]
		+	[[Category: Gizzi, A.]]
		+	[[Category: Hammonds, J.]]
		+	[[Category: Hillerich, B.]]
		+	[[Category: Kar, A.]]
		+	[[Category: LaFleur, J.]]
		+	[[Category: Love, J.]]
		+	[[Category: Morisco, L L.]]
		+	[[Category: NYSGRC, New York Structural Genomics Research Consortium.]]
		+	[[Category: Seidel, R D.]]
		+	[[Category: Sojitra, S.]]
		+	[[Category: Stead, M.]]
		+	[[Category: Toro, R.]]
		+	[[Category: Vetting, M W.]]
		+	[[Category: Villigas, G.]]
		+	[[Category: Wasserman, S R.]]
		+	[[Category: Betaine racemase]]
		+	[[Category: Enolase]]
		+	[[Category: Isomerase]]
		+	[[Category: New york structural genomics research consortium]]
		+	[[Category: Nysgrc]]
		+	[[Category: Proline betaine racemease]]
		+	[[Category: Psi-biology]]
		+	[[Category: Structural genomic]]

OCA: Protected "4j1o" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2013 10:09:23 GMT

Protected "4j1o" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:09, 13 February 2013

OCA: New page: '''Unreleased structure''' The entry 4j1o is ON HOLD Authors: Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala,S., Kar, A., LaFleur, J., Villiga...

OCA — Wed, 13 Feb 2013 10:09:22 GMT

New page: '''Unreleased structure''' The entry 4j1o is ON HOLD Authors: Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala,S., Kar, A., LaFleur, J., Villiga...

New page

'''Unreleased structure'''

The entry 4j1o is ON HOLD

Authors: Vetting, M.W., Toro, R., Bhosle, R., Wasserman, S.R., Morisco, L.L., Sojitra, S., Chamala,S., Kar, A., LaFleur, J., Villigas, G., Evans, B., Hammonds, J., Gizzi, A., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Bonanno, J.B., Gerlt, J.A., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Description: CRYSTAL STRUCTURE OF AN ENOLASE (MANDELATE RACEMASE SUBGROUP) FROM PARACOCOCUS DENITRIFICANS PD1222 (TARGET NYSGRC-012907) WITH BOUND L-PROLINE BETAINE (SUBSTRATE)