1nai - Revision history

OCA at 07:54, 14 February 2024

OCA — Wed, 14 Feb 2024 07:54:35 GMT

←Older revision		Revision as of 07:54, 14 February 2024
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	<StructureSection load='1nai' size='340' side='right'caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nai' size='340' side='right'caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nai]] is a 1 chain structure with sequence from [https://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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nai]] 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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NAI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [https://pdbe.org/1nai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [https://www.ebi.ac.uk/pdbsum/1nai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nai 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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [https://pdbe.org/1nai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [https://www.ebi.ac.uk/pdbsum/1nai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nai ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GALE_ECOLI GALE_ECOLI]
	== 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=1nai 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=1nai ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	UDP-galactose 4-epimerase catalyzes the conversion of UDP-galactose to UDP-glucose through a mechanism involving the transient reduction of NAD+. Here we describe the X-ray structures for epimerase complexed with NADH/UDP, and NAD+/UDP, refined to 1.8 and 2.0 angstrom, respectively. The alpha-carbon positions for the two forms of the enzyme are superimposed with a root-mean-square deviation of 0.36 A. Overall, the models for the reduced and oxidized proteins are very similar except for the positions of several side chains including Phe 178 and Phe 218. The most striking difference between the oxidized and reduced enzymes is the conformation of the nicotinamide ring of the dinucleotide. In the reduced protein, the nicotinamide ring adopts the anti conformation while in the oxidized enzyme the syn conformation is observed. There are also significant structural differences in UDP binding between the oxidized and reduced forms of the protein which most likely explain the observation that uridine nucleotides bind more tightly to epimerase/NADH than to epimerase/NAD+. Both van der Waals and electrostatic interactions between epimerase and NAD+ are extensive with 35 contacts below 3.2 angstrom as would be expected for enzyme that binds the dinucleotide irreversibly. This is in sharp contrast to the patterns typically observed for the NAD+-dependent dehydrogenases which bind nucleotides in a reversible fashion. While it has been postulated that the active site of epimerase must contain a base, the only potential candidates within approximately 5 A of both the NAD+ and the UDP are Asp 31, Asp 58, and ASP 295. These amino acid residues, however, are intimately involved in nucleotide binding and most likely do not play a role in the actual catalytic mechanism. Thus it may be speculated that an amino acid residue, other than glutamate, aspartate, or histidine, may be functioning as the active site base.
-
-	Crystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli.,Thoden JB, Frey PA, Holden HM Biochemistry. 1996 Feb 27;35(8):2557-66. PMID:8611559<ref>PMID:8611559</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1nai" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[UDP-galactose 4-epimerase\|UDP-galactose 4-epimerase]]		*[[UDP-galactose 4-epimerase\|UDP-galactose 4-epimerase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: UDP-glucose 4-epimerase]]~~	+	[[Category: Frey PA]]
-	[[Category: Frey~~, P A~~]]	+	[[Category: Holden HM]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Thoden JB]]
-	[[Category: Thoden~~, J B]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA at 07:00, 25 August 2021

OCA — Wed, 25 Aug 2021 07:00:19 GMT

←Older revision		Revision as of 07:00, 25 August 2021
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	<StructureSection load='1nai' size='340' side='right'caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nai' size='340' side='right'caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nai]] 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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nai]] is a 1 chain structure with sequence from [https://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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NAI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [~~http~~://pdbe.org/1nai PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1nai PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1nai 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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [https://pdbe.org/1nai PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [https://www.ebi.ac.uk/pdbsum/1nai PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nai ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 18:20, 20 November 2019

OCA — Wed, 20 Nov 2019 18:20:21 GMT

←Older revision		Revision as of 18:20, 20 November 2019
Line 1:		Line 1:

	==UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED==		==UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED==
-	<StructureSection load='1nai' size='340' side='right' caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1nai' size='340' side='right'caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nai]] 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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NAI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nai]] 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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NAI FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/na/1nai_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/na/1nai_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 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1nai" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nai" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[UDP-galactose 4-epimerase\|UDP-galactose 4-epimerase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: UDP-glucose 4-epimerase]]		[[Category: UDP-glucose 4-epimerase]]
	[[Category: Frey, P A]]		[[Category: Frey, P A]]

OCA at 06:48, 29 November 2017

OCA — Wed, 29 Nov 2017 06:48:29 GMT

←Older revision		Revision as of 06:48, 29 November 2017
Line 1:		Line 1:
		+
	==UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED==		==UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED==
	<StructureSection load='1nai' size='340' side='right' caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nai' size='340' side='right' caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [http://pdbe.org/1nai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [http://www.ebi.ac.uk/pdbsum/1nai 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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [http://pdbe.org/1nai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [http://www.ebi.ac.uk/pdbsum/1nai PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nai ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1nai" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1nai" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[UDP-galactose 4-epimerase\|UDP-galactose 4-epimerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:49, 10 February 2016

OCA — Wed, 10 Feb 2016 02:49:09 GMT

←Older revision		Revision as of 02:49, 10 February 2016
Line 15:		Line 15:
	<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=1nai ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:38, 11 September 2015

OCA — Fri, 11 Sep 2015 04:38:26 GMT

←Older revision		Revision as of 04:38, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1nai' size='340' side='right' caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1nai' size='340' side='right' caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1nai]] 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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NAI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1nai]] 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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NAI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [http://www.ebi.ac.uk/pdbsum/1nai 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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [http://pdbe.org/1nai PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [http://www.ebi.ac.uk/pdbsum/1nai PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1nai" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: UDP-glucose 4-epimerase]]		[[Category: UDP-glucose 4-epimerase]]
	[[Category: Frey, P A]]		[[Category: Frey, P A]]

OCA at 15:31, 5 January 2015

OCA — Mon, 05 Jan 2015 15:31:21 GMT

←Older revision		Revision as of 15:31, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1nai]] 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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NAI FirstGlance]. <br>		<table><tr><td colspan='2'>[[1nai]] 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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NAI FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [http://www.ebi.ac.uk/pdbsum/1nai 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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [http://www.ebi.ac.uk/pdbsum/1nai 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 34:		Line 34:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: UDP-glucose 4-epimerase]]		[[Category: UDP-glucose 4-epimerase]]
-	[[Category: Frey, P A.]]	+	[[Category: Frey, P A]]
-	[[Category: Holden, H M.]]	+	[[Category: Holden, H M]]
-	[[Category: Thoden, J B.]]	+	[[Category: Thoden, J B]]
	[[Category: Isomerase]]		[[Category: Isomerase]]

OCA at 08:25, 3 October 2014

OCA — Fri, 03 Oct 2014 08:25:49 GMT

←Older revision		Revision as of 08:25, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1nai~~\| ~~PDB~~=1nai \| ~~SCENE~~= }}	+	==UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED==
-	===UDP-~~GALACTOSE~~ 4-~~EPIMERASE FROM ESCHERICHIA COLI~~, ~~OXIDIZED~~===	+	<StructureSection load='1nai' size='340' side='right' caption='[[1nai]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~{{ABSTRACT_PUBMED_8611559}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1nai]] 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=1NAI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NAI FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=1nai FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nai OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1nai RCSB], [http://www.ebi.ac.uk/pdbsum/1nai 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/na/1nai_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 ==
		+	UDP-galactose 4-epimerase catalyzes the conversion of UDP-galactose to UDP-glucose through a mechanism involving the transient reduction of NAD+. Here we describe the X-ray structures for epimerase complexed with NADH/UDP, and NAD+/UDP, refined to 1.8 and 2.0 angstrom, respectively. The alpha-carbon positions for the two forms of the enzyme are superimposed with a root-mean-square deviation of 0.36 A. Overall, the models for the reduced and oxidized proteins are very similar except for the positions of several side chains including Phe 178 and Phe 218. The most striking difference between the oxidized and reduced enzymes is the conformation of the nicotinamide ring of the dinucleotide. In the reduced protein, the nicotinamide ring adopts the anti conformation while in the oxidized enzyme the syn conformation is observed. There are also significant structural differences in UDP binding between the oxidized and reduced forms of the protein which most likely explain the observation that uridine nucleotides bind more tightly to epimerase/NADH than to epimerase/NAD+. Both van der Waals and electrostatic interactions between epimerase and NAD+ are extensive with 35 contacts below 3.2 angstrom as would be expected for enzyme that binds the dinucleotide irreversibly. This is in sharp contrast to the patterns typically observed for the NAD+-dependent dehydrogenases which bind nucleotides in a reversible fashion. While it has been postulated that the active site of epimerase must contain a base, the only potential candidates within approximately 5 A of both the NAD+ and the UDP are Asp 31, Asp 58, and ASP 295. These amino acid residues, however, are intimately involved in nucleotide binding and most likely do not play a role in the actual catalytic mechanism. Thus it may be speculated that an amino acid residue, other than glutamate, aspartate, or histidine, may be functioning as the active site base.

-	~~==About this Structure==~~	+	Crystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli.,Thoden JB, Frey PA, Holden HM Biochemistry. 1996 Feb 27;35(8):2557-66. PMID:8611559<ref>PMID:8611559</ref>
-	~~[[1nai]] 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=1NAI OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[UDP-galactose 4-epimerase\|UDP-galactose 4-epimerase]]		*[[UDP-galactose 4-epimerase\|UDP-galactose 4-epimerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:008611559</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: UDP-glucose 4-epimerase]]		[[Category: UDP-glucose 4-epimerase]]

OCA at 10:50, 16 April 2014

OCA — Wed, 16 Apr 2014 10:50:03 GMT

←Older revision		Revision as of 10:50, 16 April 2014
Line 1:		Line 1:
-	[[Image:1nai.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1nai", 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_1nai\| PDB=1nai \| SCENE= }}		{{STRUCTURE_1nai\| PDB=1nai \| SCENE= }}
-
	===UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED===		===UDP-GALACTOSE 4-EPIMERASE FROM ESCHERICHIA COLI, OXIDIZED===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_8611559}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 8611559 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_8611559}}		{{ABSTRACT_PUBMED_8611559}}

	==About this Structure==		==About this Structure==
	[[1nai]] 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=1NAI OCA].		[[1nai]] 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=1NAI OCA].
		+
		+	==See Also==
		+	*[[UDP-galactose 4-epimerase\|UDP-galactose 4-epimerase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:008611559</ref><references group="xtra"/>	+	<ref group="xtra">PMID:008611559</ref><references group="xtra"/><references/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: UDP-glucose 4-epimerase]]		[[Category: UDP-glucose 4-epimerase]]

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

OCA — Wed, 16 Nov 2011 10:06:07 GMT

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

←Older revision

Revision as of 10:06, 16 November 2011