4e8g - Revision history

OCA at 14:55, 14 March 2024

2024-03-14T14:55:16Z

←Older revision		Revision as of 14:55, 14 March 2024
Line 10:		Line 10:
	== 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 4e8g" style="background-color:#fffaf0;"></div>

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

OCA at 08:21, 6 December 2023

2023-12-06T08:21:25Z

←Older revision		Revision as of 08:21, 6 December 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4e8g]] 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=4E8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8G FirstGlance]. <br>		<table><tr><td colspan='2'>[[4e8g]] 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=4E8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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=4e8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8g OCA], [https://pdbe.org/4e8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8g RCSB], [https://www.ebi.ac.uk/pdbsum/4e8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8g 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=4e8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8g OCA], [https://pdbe.org/4e8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8g RCSB], [https://www.ebi.ac.uk/pdbsum/4e8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8g 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 21:

	==See Also==		==See Also==
		+	*[[Enolase 3D structures\|Enolase 3D structures]]
	*[[Mandelate racemase\|Mandelate racemase]]		*[[Mandelate racemase\|Mandelate racemase]]
	*[[Mandelate racemase/muconate lactonizing enzyme 3D structures\|Mandelate racemase/muconate lactonizing enzyme 3D structures]]		*[[Mandelate racemase/muconate lactonizing enzyme 3D structures\|Mandelate racemase/muconate lactonizing enzyme 3D structures]]

OCA at 06:57, 28 September 2022

2022-09-28T06:57:16Z

←Older revision		Revision as of 06:57, 28 September 2022
Line 1:		Line 1:

	==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg==		==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg==
-	<StructureSection load='4e8g' size='340' side='right' caption='[[4e8g]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='4e8g' size='340' side='right'caption='[[4e8g]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4e8g]] 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=4E8G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4E8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4e8g]] 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=4E8G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E8G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=~~UNL~~:~~UNKNOWN+LIGAND~~'>~~UNL~~</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</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=4e8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8g OCA], [https://pdbe.org/4e8g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e8g RCSB], [https://www.ebi.ac.uk/pdbsum/4e8g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8g ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_1187 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])~~</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=4e8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8g OCA], [~~http~~://pdbe.org/4e8g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4e8g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4e8g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8g 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 20:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4e8g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4e8g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Mandelate racemase\|Mandelate racemase]]
		+	*[[Mandelate racemase/muconate lactonizing enzyme 3D structures\|Mandelate racemase/muconate lactonizing enzyme 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pardp~~]]	+	[[Category: Large Structures]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Paracoccus denitrificans PD1222]]
-	[[Category: Bhosle, R]]	+	[[Category: Almo SC]]
-	[[Category: Bonanno~~, J B~~]]	+	[[Category: Bhosle R]]
-	[[Category: Chamala, S]]	+	[[Category: Bonanno JB]]
-	[[Category: Evans, B]]	+	[[Category: Chamala S]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Evans B]]
-	[[Category: Gizzi, A]]	+	[[Category: Gerlt JA]]
-	[[Category: Hammonds, J]]	+	[[Category: Gizzi A]]
-	[[Category: Hillerich, B]]	+	[[Category: Hammonds J]]
-	[[Category: Kar, A]]	+	[[Category: Hillerich B]]
-	[[Category: Lafleur, J]]	+	[[Category: Kar A]]
-	[[Category: Love, J]]	+	[[Category: Lafleur J]]
-	[[Category: Morisco~~, L L]]~~	+	[[Category: Love J]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Morisco LL]]
-	[[Category: Seidel~~, R D~~]]	+	[[Category: Seidel RD]]
-	[[Category: Sojitra, S]]	+	[[Category: Sojitra S]]
-	[[Category: Toro, R]]	+	[[Category: Toro R]]
-	[[Category: Vetting~~, M W~~]]	+	[[Category: Vetting MW]]
-	[[Category: Villigas, G]]	+	[[Category: Villigas G]]
-	[[Category: Wasserman~~, S R~~]]	+	[[Category: Wasserman SR]]
-	[[Category: Zencheck~~, W D]]~~	+	[[Category: Zencheck WD]]
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Nysgrc]]~~	+
-	~~[[Category: Psi-biology]]~~	+
-	~~[[Category: Putative racemase~~]]	+

OCA at 19:52, 24 January 2018

2018-01-24T19:52:45Z

←Older revision		Revision as of 19:52, 24 January 2018
Line 11:		Line 11:
	== 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.

-	==~~See Also==~~	+	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>
-	*[[Mandelate racemase\|Mandelate racemase]]	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4e8g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:20, 4 August 2016

2016-08-04T08:20:26Z

←Older revision		Revision as of 08:20, 4 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg==		==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg==
	<StructureSection load='4e8g' size='340' side='right' caption='[[4e8g]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4e8g' size='340' side='right' caption='[[4e8g]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4e8g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Paracoccus_denitrificans Paracoccus denitrificans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E8G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4e8g]] 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=4E8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E8G FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_1187 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~266 Paracoccus denitrificans~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_1187 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=318586 PARDP])</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=4e8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e8g RCSB], [http://www.ebi.ac.uk/pdbsum/4e8g 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=4e8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8g OCA], [http://pdbe.org/4e8g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e8g RCSB], [http://www.ebi.ac.uk/pdbsum/4e8g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e8g 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>

	==See Also==		==See Also==
Line 17:		Line 18:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Paracoccus denitrificans~~]]	+	[[Category: Pardp]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]
	[[Category: Bhosle, R]]		[[Category: Bhosle, R]]

OCA at 07:17, 25 December 2014

2014-12-25T07:17:43Z

←Older revision		Revision as of 07:17, 25 December 2014
Line 8:		Line 8:
	<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=4e8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e8g RCSB], [http://www.ebi.ac.uk/pdbsum/4e8g 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=4e8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e8g RCSB], [http://www.ebi.ac.uk/pdbsum/4e8g PDBsum]</span></td></tr>
	</table>		</table>
		+	== 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>

	==See Also==		==See Also==
	*[[Mandelate racemase\|Mandelate racemase]]		*[[Mandelate racemase\|Mandelate racemase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:45, 18 December 2014

2014-12-18T08:45:01Z

←Older revision		Revision as of 08:45, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4e8g\| PDB=4e8g \| SCENE= }}~~	+	==Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg==
-	===Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg===	+	<StructureSection load='4e8g' size='340' side='right' caption='[[4e8g]], [[Resolution\|resolution]] 2.00Å' scene=''>
-		+	== Structural highlights ==
-	==~~About this Structure~~==	+	<table><tr><td colspan='2'>[[4e8g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E8G FirstGlance]. <br>
-	[[4e8g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8G OCA].	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pden_1187 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=266 Paracoccus denitrificans])</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=4e8g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e8g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e8g RCSB], [http://www.ebi.ac.uk/pdbsum/4e8g PDBsum]</span></td></tr>
		+	</table>

	==See Also==		==See Also==
	*[[Mandelate racemase\|Mandelate racemase]]		*[[Mandelate racemase\|Mandelate racemase]]
		+	__TOC__
		+	</StructureSection>
	[[Category: Paracoccus denitrificans]]		[[Category: Paracoccus denitrificans]]
-	[[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: 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: Zencheck, W D.]]	+	[[Category: Zencheck, W D]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
-	[[Category: New york structural genomics research consortium]]
	[[Category: Nysgrc]]		[[Category: Nysgrc]]
	[[Category: Psi-biology]]		[[Category: Psi-biology]]
	[[Category: Putative racemase]]		[[Category: Putative racemase]]
-	[[Category: Structural genomic]]

OCA at 09:36, 11 March 2013

2013-03-11T09:36:04Z

←Older revision		Revision as of 09:36, 11 March 2013
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-	[[Image:4e8g.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_4e8g", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_4e8g\| PDB=4e8g \| SCENE= }}		{{STRUCTURE_4e8g\| PDB=4e8g \| SCENE= }}
-
	===Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg===		===Crystal structure of an enolase (mandelate racemase subgroup) from paracococus denitrificans pd1222 (target nysgrc-012907) with bound mg===
-

	==About this Structure==		==About this Structure==
	[[4e8g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8G OCA].		[[4e8g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8G OCA].
		+
		+	==See Also==
		+	*[[Mandelate racemase\|Mandelate racemase]]
	[[Category: Paracoccus denitrificans]]		[[Category: Paracoccus denitrificans]]
	[[Category: Almo, S C.]]		[[Category: Almo, S C.]]

OCA at 19:29, 2 May 2012

2012-05-02T19:29:56Z

←Older revision		Revision as of 19:29, 2 May 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4e8g.jpg\|left\|200px]]

-	The ~~entry 4e8g~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_4e8g", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_4e8g\| PDB=4e8g \| 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., Zencheck, W.D., 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 mg===

-	~~Description: Crystal~~ structure ~~of an enolase (mandelate racemase subgroup)~~ from ~~paracococus~~ denitrificans ~~pd1222 (target nysgrc~~-~~012907) with bound mg~~	+
		+	==About this Structure==
		+	[[4e8g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E8G OCA].
		+	[[Category: Paracoccus denitrificans]]
		+	[[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: Toro, R.]]
		+	[[Category: Vetting, M W.]]
		+	[[Category: Villigas, G.]]
		+	[[Category: Wasserman, S R.]]
		+	[[Category: Zencheck, W D.]]
		+	[[Category: Isomerase]]
		+	[[Category: New york structural genomics research consortium]]
		+	[[Category: Nysgrc]]
		+	[[Category: Psi-biology]]
		+	[[Category: Putative racemase]]
		+	[[Category: Structural genomic]]

OCA: Protected "4e8g" [edit=sysop:move=sysop]

2012-03-28T07:24:28Z

Protected "4e8g" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:24, 28 March 2012