1tj2 - Revision history

OCA at 06:30, 23 August 2023

OCA — Wed, 23 Aug 2023 06:30:36 GMT

←Older revision		Revision as of 06:30, 23 August 2023
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	<StructureSection load='1tj2' size='340' side='right'caption='[[1tj2]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1tj2' size='340' side='right'caption='[[1tj2]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tj2]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1TJ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tj2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TJ2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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]] 2.05Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1tiw\|1tiw]], [[1tj0\|1tj0]], [[1k87\|1k87]], [[1tj1\|1tj1]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PUTA, POAA, B1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</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=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [https://pdbe.org/1tj2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [https://www.ebi.ac.uk/pdbsum/1tj2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tj2 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/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [~~http~~://pdbe.org/1tj2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1tj2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1tj2 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PUTA_ECOLI PUTA_ECOLI]] Oxidizes proline to glutamate for use as a carbon and nitrogen source and also function as a transcriptional repressor of the put operon.	+	[https://www.uniprot.org/uniprot/PUTA_ECOLI PUTA_ECOLI] Oxidizes proline to glutamate for use as a carbon and nitrogen source and also function as a transcriptional repressor of the put operon.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 38:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Proline dehydrogenase]]~~	+	[[Category: Baban BA]]
-	[[Category: Baban~~, B A~~]]	+	[[Category: Becker DF]]
-	[[Category: Becker~~, D F~~]]	+	[[Category: Schuermann JP]]
-	[[Category: Schuermann~~, J P~~]]	+	[[Category: Tanner JJ]]
-	[[Category: Tanner~~, J J~~]]	+	[[Category: White TA]]
-	[[Category: White~~, T A~~]]	+	[[Category: Zhang M]]
-	[[Category: Zhang, M]]	+
-	~~[[Category: Beta/alpha barrel]]~~	+
-	~~[[Category: Fad]]~~	+
-	~~[[Category: Flavoenzyme]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Proline catabolism~~]]	+

OCA at 11:52, 24 December 2020

OCA — Thu, 24 Dec 2020 11:52:52 GMT

←Older revision		Revision as of 11:52, 24 December 2020
Line 1:		Line 1:

	==Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with acetate==		==Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with acetate==
-	<StructureSection load='1tj2' size='340' side='right' caption='[[1tj2]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='1tj2' size='340' side='right'caption='[[1tj2]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tj2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TJ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tj2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1TJ2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tiw\|1tiw]], [[1tj0\|1tj0]], [[1k87\|1k87]], [[1tj1\|1tj1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1tiw\|1tiw]], [[1tj0\|1tj0]], [[1k87\|1k87]], [[1tj1\|1tj1]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PUTA, POAA, B1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PUTA, POAA, B1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8] </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=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [http://pdbe.org/1tj2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [http://www.ebi.ac.uk/pdbsum/1tj2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tj2 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [http://pdbe.org/1tj2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [http://www.ebi.ac.uk/pdbsum/1tj2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tj2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Proline dehydrogenase]]		[[Category: Proline dehydrogenase]]
	[[Category: Baban, B A]]		[[Category: Baban, B A]]

OCA at 08:44, 21 March 2018

OCA — Wed, 21 Mar 2018 08:44:53 GMT

←Older revision		Revision as of 08:44, 21 March 2018
Line 1:		Line 1:
		+
	==Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with acetate==		==Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with acetate==
	<StructureSection load='1tj2' size='340' side='right' caption='[[1tj2]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1tj2' size='340' side='right' caption='[[1tj2]], [[Resolution\|resolution]] 2.05Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PUTA, POAA, B1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PUTA, POAA, B1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8] </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=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [http://pdbe.org/1tj2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [http://www.ebi.ac.uk/pdbsum/1tj2 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=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [http://pdbe.org/1tj2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [http://www.ebi.ac.uk/pdbsum/1tj2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tj2 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tj/1tj2_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tj/1tj2_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 13:18, 8 February 2016

OCA — Mon, 08 Feb 2016 13:18:11 GMT

←Older revision		Revision as of 13:18, 8 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1tj2 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 11:56, 10 September 2015

OCA — Thu, 10 Sep 2015 11:56:49 GMT

←Older revision		Revision as of 11:56, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1tj2' size='340' side='right' caption='[[1tj2]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='1tj2' size='340' side='right' caption='[[1tj2]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tj2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TJ2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tj2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TJ2 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tiw\|1tiw]], [[1tj0\|1tj0]], [[1k87\|1k87]], [[1tj1\|1tj1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tiw\|1tiw]], [[1tj0\|1tj0]], [[1k87\|1k87]], [[1tj1\|1tj1]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PUTA, POAA, B1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PUTA, POAA, B1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8] </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=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [http://www.ebi.ac.uk/pdbsum/1tj2 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=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [http://pdbe.org/1tj2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [http://www.ebi.ac.uk/pdbsum/1tj2 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1tj2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Proline utilization A\|Proline utilization A]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Proline dehydrogenase]]		[[Category: Proline dehydrogenase]]
	[[Category: Baban, B A]]		[[Category: Baban, B A]]

OCA at 23:35, 24 December 2014

OCA — Wed, 24 Dec 2014 23:35:51 GMT

←Older revision		Revision as of 23:35, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tj2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TJ2 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tj2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TJ2 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tiw\|1tiw]], [[1tj0\|1tj0]], [[1k87\|1k87]], [[1tj1\|1tj1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tiw\|1tiw]], [[1tj0\|1tj0]], [[1k87\|1k87]], [[1tj1\|1tj1]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PUTA, POAA, B1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PUTA, POAA, B1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [http://www.ebi.ac.uk/pdbsum/1tj2 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=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [http://www.ebi.ac.uk/pdbsum/1tj2 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PUTA_ECOLI PUTA_ECOLI]] Oxidizes proline to glutamate for use as a carbon and nitrogen source and also function as a transcriptional repressor of the put operon.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Proline dehydrogenase]]		[[Category: Proline dehydrogenase]]
-	[[Category: Baban, B A.]]	+	[[Category: Baban, B A]]
-	[[Category: Becker, D F.]]	+	[[Category: Becker, D F]]
-	[[Category: Schuermann, J P.]]	+	[[Category: Schuermann, J P]]
-	[[Category: Tanner, J J.]]	+	[[Category: Tanner, J J]]
-	[[Category: White, T A.]]	+	[[Category: White, T A]]
-	[[Category: Zhang, M.]]	+	[[Category: Zhang, M]]
	[[Category: Beta/alpha barrel]]		[[Category: Beta/alpha barrel]]
	[[Category: Fad]]		[[Category: Fad]]

OCA at 19:34, 29 September 2014

OCA — Mon, 29 Sep 2014 19:34:46 GMT

←Older revision		Revision as of 19:34, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1tj2.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with acetate==
		+	<StructureSection load='1tj2' size='340' side='right' caption='[[1tj2]], [[Resolution\|resolution]] 2.05Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1tj2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TJ2 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tiw\|1tiw]], [[1tj0\|1tj0]], [[1k87\|1k87]], [[1tj1\|1tj1]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PUTA, POAA, B1014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Proline_dehydrogenase Proline dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.99.8 1.5.99.8] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1tj2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tj2 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tj2 RCSB], [http://www.ebi.ac.uk/pdbsum/1tj2 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tj/1tj2_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proline dehydrogenase (PRODH) catalyzes the first step of proline catabolism, the flavin-dependent oxidation of proline to Delta(1)-pyrroline-5-carboxylate. Here we present a structure-based study of the PRODH active site of the multifunctional Escherichia coli proline utilization A (PutA) protein using X-ray crystallography, enzyme kinetic measurements, and site-directed mutagenesis. Structures of the PutA PRODH domain complexed with competitive inhibitors acetate (K(i) = 30 mM), L-lactate (K(i) = 1 mM), and L-tetrahydro-2-furoic acid (L-THFA, K(i) = 0.2 mM) have been determined to high-resolution limits of 2.1-2.0 A. The discovery of acetate as a competitive inhibitor suggests that the carboxyl is the minimum functional group recognized by the active site, and the structures show how the enzyme exploits hydrogen-bonding and nonpolar interactions to optimize affinity for the substrate. The PRODH/L-THFA complex is the first structure of PRODH with a five-membered ring proline analogue bound in the active site and thus provides new insights into substrate recognition and the catalytic mechanism. The ring of L-THFA is nearly parallel to the middle ring of the FAD isoalloxazine, with the inhibitor C5 atom 3.3 A from the FAD N5. This geometry suggests direct hydride transfer as a plausible mechanism. Mutation of conserved active site residue Leu432 to Pro caused a 5-fold decrease in k(cat) and a severe loss in thermostability. These changes are consistent with the location of Leu432 in the hydrophobic core near residues that directly contact FAD. Our results suggest that the molecular basis for increased plasma proline levels in schizophrenic subjects carrying the missense mutation L441P is due to decreased stability of human PRODH2.

-	~~{{STRUCTURE_1tj2\| PDB=1tj2 \| SCENE= }}~~	+	Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors.,Zhang M, White TA, Schuermann JP, Baban BA, Becker DF, Tanner JJ Biochemistry. 2004 Oct 5;43(39):12539-48. PMID:15449943<ref>PMID:15449943</ref>

-	~~===Crystal structure~~ of E. ~~coli PutA proline dehydrogenase domain (residues 86-669) complexed with acetate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15449943}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1tj2]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015449943<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Proline dehydrogenase]]		[[Category: Proline dehydrogenase]]

OCA: Protected "1tj2" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 12:45:19 GMT

Protected "1tj2" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:45, 5 January 2013

OCA at 12:45, 5 January 2013

OCA — Sat, 05 Jan 2013 12:45:17 GMT

←Older revision		Revision as of 12:45, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1tj2.png\|left\|200px]]		[[Image:1tj2.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1tj2", 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_1tj2\| PDB=1tj2 \| SCENE= }}		{{STRUCTURE_1tj2\| PDB=1tj2 \| SCENE= }}

	===Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with acetate===		===Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with acetate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15449943}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15449943 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15449943}}		{{ABSTRACT_PUBMED_15449943}}

	==About this Structure==		==About this Structure==
-	~~1TJ2~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA].	+	[[1tj2]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15449943~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015449943</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Proline dehydrogenase]]		[[Category: Proline dehydrogenase]]
Line 35:		Line 23:
	[[Category: Fad]]		[[Category: Fad]]
	[[Category: Flavoenzyme]]		[[Category: Flavoenzyme]]
		+	[[Category: Oxidoreductase]]
	[[Category: Proline catabolism]]		[[Category: Proline catabolism]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 22:22:48 2009''

OCA at 20:22, 16 February 2009

OCA — Mon, 16 Feb 2009 20:22:49 GMT

←Older revision		Revision as of 20:22, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1TJ2 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA].	+	1TJ2 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TJ2 OCA].

	==Reference==		==Reference==
-	Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors., Zhang M, White TA, Schuermann JP, Baban BA, Becker DF, Tanner JJ, Biochemistry. 2004 Oct 5;43(39):12539-48. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15449943 15449943]~~	+	<ref group="xtra">PMID:15449943</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Proline dehydrogenase]]		[[Category: Proline dehydrogenase]]
-	[[Category: Single protein]]
	[[Category: Baban, B A.]]		[[Category: Baban, B A.]]
	[[Category: Becker, D F.]]		[[Category: Becker, D F.]]
Line 38:		Line 37:
	[[Category: Proline catabolism]]		[[Category: Proline catabolism]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 03~~:22:~~52 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 22:22:48 2009''