1bqg - Revision history

OCA at 06:38, 7 February 2024

2024-02-07T06:38:23Z

←Older revision		Revision as of 06:38, 7 February 2024
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	<StructureSection load='1bqg' size='340' side='right'caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1bqg' size='340' side='right'caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BQG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BQG FirstGlance]. <br>
-	</td></tr><tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"~~><span class~~=~~'plainlinks'~~>[~~https://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase~~]~~, with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.~~2.~~1.40 4.2.1.40] </span>~~</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]] 2.3Å</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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [https://pdbe.org/1bqg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [https://www.ebi.ac.uk/pdbsum/1bqg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bqg 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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [https://pdbe.org/1bqg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [https://www.ebi.ac.uk/pdbsum/1bqg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bqg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GUDD_PSEPU GUDD_PSEPU]] Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc).	+	[https://www.uniprot.org/uniprot/GUDD_PSEPU GUDD_PSEPU] Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1bqg 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=1bqg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of (D)-glucarate dehydratase from Pseudomonas putida (GlucD) has been solved at 2.3 A resolution by multiple isomorphous replacement and refined to a final R-factor of 19.0%. The protein crystallizes in the space group I222 with one subunit in the asymmetric unit. The unit cell dimensions are a = 69.6 A, b = 108.8 A, and c = 122.6 A. The crystals were grown using the batch method where the primary precipitant was poly(ethylene glycol) 1000. The structure reveals that GlucD is a tetramer of four identical polypeptides, each containing 451 residues. The structure was determined without a bound substrate or substrate analogue. Three disordered regions are noted: the N-terminus through residue 11, a loop containing residues 99 through 110, and the C-terminus from residue 423. On the basis of primary sequence alignments, we previously concluded that GlucD is a member of the mandelate racemase (MR) subfamily of the enolase superfamily [Babbitt, P. C., Hasson, M. S., Wedekind, J. E., Palmer, D. R. J., Barrett, W. C., Reed, G. J., Rayment, I., Ringe, D., Kenyon, G. L., and Gerlt, J. A. (1996) Biochemistry 35, 16489-16501]. This prediction is now verified, since the overall fold of GlucD is strikingly similar to those of MR, muconate lactonizing enzyme I, and enolase. Also, many of the active site residues of GlucD can be superimposed on those found in the active site of MR. The implications of this structure on the evolution of catalysis in the enolase superfamily are discussed.
-
-	Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.,Gulick AM, Palmer DR, Babbitt PC, Gerlt JA, Rayment I Biochemistry. 1998 Oct 13;37(41):14358-68. PMID:9772161<ref>PMID:9772161</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1bqg" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus fluorescens putidus flugge 1886]]
-	[[Category: Glucarate dehydratase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Babbitt, P C~~]]	+	[[Category: Pseudomonas putida]]
-	[[Category: ~~Gerlt, J A~~]]	+	[[Category: Babbitt PC]]
-	[[Category: ~~Gulick, A M~~]]	+	[[Category: Gerlt JA]]
-	[[Category: ~~Palmer, D R.J~~]]	+	[[Category: Gulick AM]]
-	[[Category: ~~Rayment, I~~]]	+	[[Category: Palmer DRJ]]
-	[[Category: ~~Enolase superfamily]]~~	+	[[Category: Rayment I]]
-	~~[[Category: Glucarate]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 10:28, 14 July 2021

2021-07-14T10:28:14Z

←Older revision		Revision as of 10:28, 14 July 2021
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	<StructureSection load='1bqg' size='340' side='right'caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1bqg' size='340' side='right'caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1BQG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BQG FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] </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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [~~http~~://pdbe.org/1bqg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1bqg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1bqg 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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [https://pdbe.org/1bqg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [https://www.ebi.ac.uk/pdbsum/1bqg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bqg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GUDD_PSEPU GUDD_PSEPU]] Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc).	+	[[https://www.uniprot.org/uniprot/GUDD_PSEPU GUDD_PSEPU]] Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:44, 10 October 2019

2019-10-10T06:44:50Z

←Older revision		Revision as of 06:44, 10 October 2019
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	==THE STRUCTURE OF THE D-GLUCARATE DEHYDRATASE PROTEIN FROM PSEUDOMONAS PUTIDA==		==THE STRUCTURE OF THE D-GLUCARATE DEHYDRATASE PROTEIN FROM PSEUDOMONAS PUTIDA==
-	<StructureSection load='1bqg' size='340' side='right' caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1bqg' size='340' side='right'caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQG FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bq/1bqg_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bq/1bqg_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>
Line 34:		Line 34:
	[[Category: Bacillus fluorescens putidus flugge 1886]]		[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Glucarate dehydratase]]		[[Category: Glucarate dehydratase]]
		+	[[Category: Large Structures]]
	[[Category: Babbitt, P C]]		[[Category: Babbitt, P C]]
	[[Category: Gerlt, J A]]		[[Category: Gerlt, J A]]

OCA at 08:08, 29 November 2017

2017-11-29T08:08:37Z

←Older revision		Revision as of 08:08, 29 November 2017
Line 1:		Line 1:
		+
	==THE STRUCTURE OF THE D-GLUCARATE DEHYDRATASE PROTEIN FROM PSEUDOMONAS PUTIDA==		==THE STRUCTURE OF THE D-GLUCARATE DEHYDRATASE PROTEIN FROM PSEUDOMONAS PUTIDA==
	<StructureSection load='1bqg' size='340' side='right' caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1bqg' size='340' side='right' caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>
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	<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQG FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] </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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [http://pdbe.org/1bqg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [http://www.ebi.ac.uk/pdbsum/1bqg 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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [http://pdbe.org/1bqg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [http://www.ebi.ac.uk/pdbsum/1bqg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bqg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 00:17, 8 February 2016

2016-02-08T00:17:40Z

←Older revision		Revision as of 00:17, 8 February 2016
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	<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=1bqg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:09, 10 September 2015

2015-09-10T06:09:05Z

←Older revision		Revision as of 06:09, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1bqg' size='340' side='right' caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1bqg' size='340' side='right' caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pseudomonas_putida Pseudomonas putida~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQG FirstGlance]. <br>
	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] </span></td></tr>		</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] </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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [http://www.ebi.ac.uk/pdbsum/1bqg 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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [http://pdbe.org/1bqg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [http://www.ebi.ac.uk/pdbsum/1bqg PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~GUDH_PSEPU GUDH_PSEPU~~]] Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc).	+	[[http://www.uniprot.org/uniprot/GUDD_PSEPU GUDD_PSEPU]] Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 26:		Line 26:
	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 1bqg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus fluorescens putidus flugge 1886]]
	[[Category: Glucarate dehydratase]]		[[Category: Glucarate dehydratase]]
-	[[Category: Pseudomonas putida]]
	[[Category: Babbitt, P C]]		[[Category: Babbitt, P C]]
	[[Category: Gerlt, J A]]		[[Category: Gerlt, J A]]

OCA at 19:12, 24 December 2014

2014-12-24T19:12:06Z

←Older revision		Revision as of 19:12, 24 December 2014
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	<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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [http://www.ebi.ac.uk/pdbsum/1bqg 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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [http://www.ebi.ac.uk/pdbsum/1bqg PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GUDH_PSEPU GUDH_PSEPU]] Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:30, 22 December 2014

2014-12-22T11:30:21Z

←Older revision		Revision as of 11:30, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQG FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQG FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] </span></td></tr>	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] </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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [http://www.ebi.ac.uk/pdbsum/1bqg 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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [http://www.ebi.ac.uk/pdbsum/1bqg PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	[[Category: Glucarate dehydratase]]		[[Category: Glucarate dehydratase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]
-	[[Category: Babbitt, P C.]]	+	[[Category: Babbitt, P C]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
-	[[Category: Gulick, A M.]]	+	[[Category: Gulick, A M]]
-	[[Category: Palmer, D R.J.]]	+	[[Category: Palmer, D R.J]]
-	[[Category: Rayment, I.]]	+	[[Category: Rayment, I]]
	[[Category: Enolase superfamily]]		[[Category: Enolase superfamily]]
	[[Category: Glucarate]]		[[Category: Glucarate]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

OCA at 09:39, 13 August 2014

2014-08-13T09:39:12Z

←Older revision		Revision as of 09:39, 13 August 2014
Line 1:		Line 1:
-	[[~~Image~~:1bqg.~~png\|left~~\|200px]]	+	==THE STRUCTURE OF THE D-GLUCARATE DEHYDRATASE PROTEIN FROM PSEUDOMONAS PUTIDA==
		+	<StructureSection load='1bqg' size='340' side='right' caption='[[1bqg]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1bqg]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQG FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucarate_dehydratase Glucarate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.40 4.2.1.40] </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=1bqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bqg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bqg RCSB], [http://www.ebi.ac.uk/pdbsum/1bqg 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/bq/1bqg_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 ==
		+	The structure of (D)-glucarate dehydratase from Pseudomonas putida (GlucD) has been solved at 2.3 A resolution by multiple isomorphous replacement and refined to a final R-factor of 19.0%. The protein crystallizes in the space group I222 with one subunit in the asymmetric unit. The unit cell dimensions are a = 69.6 A, b = 108.8 A, and c = 122.6 A. The crystals were grown using the batch method where the primary precipitant was poly(ethylene glycol) 1000. The structure reveals that GlucD is a tetramer of four identical polypeptides, each containing 451 residues. The structure was determined without a bound substrate or substrate analogue. Three disordered regions are noted: the N-terminus through residue 11, a loop containing residues 99 through 110, and the C-terminus from residue 423. On the basis of primary sequence alignments, we previously concluded that GlucD is a member of the mandelate racemase (MR) subfamily of the enolase superfamily [Babbitt, P. C., Hasson, M. S., Wedekind, J. E., Palmer, D. R. J., Barrett, W. C., Reed, G. J., Rayment, I., Ringe, D., Kenyon, G. L., and Gerlt, J. A. (1996) Biochemistry 35, 16489-16501]. This prediction is now verified, since the overall fold of GlucD is strikingly similar to those of MR, muconate lactonizing enzyme I, and enolase. Also, many of the active site residues of GlucD can be superimposed on those found in the active site of MR. The implications of this structure on the evolution of catalysis in the enolase superfamily are discussed.

-	~~{{STRUCTURE_1bqg\| PDB=1bqg \| SCENE= }}~~	+	Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida.,Gulick AM, Palmer DR, Babbitt PC, Gerlt JA, Rayment I Biochemistry. 1998 Oct 13;37(41):14358-68. PMID:9772161<ref>PMID:9772161</ref>

-	~~===THE STRUCTURE OF THE D-GLUCARATE DEHYDRATASE PROTEIN FROM PSEUDOMONAS PUTIDA===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9772161}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1bqg]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pseudomonas_putida Pseudomonas putida]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1BQG OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009772161<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Glucarate dehydratase]]		[[Category: Glucarate dehydratase]]
	[[Category: Pseudomonas putida]]		[[Category: Pseudomonas putida]]

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

2012-10-21T20:07:03Z

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

←Older revision

Revision as of 20:07, 21 October 2012