2b5w - Revision history

OCA at 07:34, 23 August 2023

OCA — Wed, 23 Aug 2023 07:34:20 GMT

←Older revision		Revision as of 07:34, 23 August 2023
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	<StructureSection load='2b5w' size='340' side='right'caption='[[2b5w]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2b5w' size='340' side='right'caption='[[2b5w]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2b5w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_33500 Atcc 33500~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2b5w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloferax_mediterranei Haloferax mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B5W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b5v\|2b5v]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gdh ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 ATCC 33500])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [https://pdbe.org/2b5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [https://www.ebi.ac.uk/pdbsum/2b5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b5w 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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [https://pdbe.org/2b5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [https://www.ebi.ac.uk/pdbsum/2b5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b5w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GLCDH_HALMT GLCDH_HALMT]] Catalyzes the NAD(P)(+)-dependent oxidation of D-glucose to D-gluconate. Displays broad substrate specificity since it is able to catalyze the oxidation of a number of alternative aldose sugars, such as D-xylose, D-galactose, and D-fucose, to the corresponding glyconate. Can utilize both NAD(+) and NADP(+) as electron acceptor, with a preference for NADP(+). Physiologically, seems to be involved in the degradation of glucose through a modified Entner-Doudoroff pathway.<ref>PMID:11425479</ref> <ref>PMID:8925901</ref>	+	[https://www.uniprot.org/uniprot/GLCDH_HALMT GLCDH_HALMT] Catalyzes the NAD(P)(+)-dependent oxidation of D-glucose to D-gluconate. Displays broad substrate specificity since it is able to catalyze the oxidation of a number of alternative aldose sugars, such as D-xylose, D-galactose, and D-fucose, to the corresponding glyconate. Can utilize both NAD(+) and NADP(+) as electron acceptor, with a preference for NADP(+). Physiologically, seems to be involved in the degradation of glucose through a modified Entner-Doudoroff pathway.<ref>PMID:11425479</ref> <ref>PMID:8925901</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 33500]]~~	+	[[Category: Haloferax mediterranei]]
-	~~[[Category: Glucose 1-dehydrogenase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baker~~, P J~~]]	+	[[Category: Baker PJ]]
-	[[Category: Bonete, M J]]	+	[[Category: Bonete M-J]]
-	[[Category: Britton~~, K L~~]]	+	[[Category: Britton KL]]
-	[[Category: Esclapez, J]]	+	[[Category: Esclapez J]]
-	[[Category: Ferrer, J]]	+	[[Category: Ferrer J]]
-	[[Category: Fisher, M]]	+	[[Category: Fisher M]]
-	[[Category: Gilmour~~, D J~~]]	+	[[Category: Gilmour DJ]]
-	[[Category: Pire, C]]	+	[[Category: Pire C]]
-	[[Category: Rice~~, D W~~]]	+	[[Category: Rice DW]]
-	[[Category: Ruzheinikov, S]]	+	[[Category: Ruzheinikov S]]
-	~~[[Category: Nucleotide binding motif]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:36, 3 February 2021

OCA — Wed, 03 Feb 2021 11:36:17 GMT

←Older revision		Revision as of 11:36, 3 February 2021
Line 1:		Line 1:

	==Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei==		==Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei==
-	<StructureSection load='2b5w' size='340' side='right' caption='[[2b5w]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='2b5w' size='340' side='right'caption='[[2b5w]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2b5w]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_33500 Atcc 33500]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2B5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2b5w]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_33500 Atcc 33500]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B5W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5v\|2b5v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b5v\|2b5v]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gdh ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 ATCC 33500])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gdh ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 ATCC 33500])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [~~http~~://pdbe.org/2b5w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2b5w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2b5w 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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [https://pdbe.org/2b5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [https://www.ebi.ac.uk/pdbsum/2b5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b5w ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GLCDH_HALMT GLCDH_HALMT]] Catalyzes the NAD(P)(+)-dependent oxidation of D-glucose to D-gluconate. Displays broad substrate specificity since it is able to catalyze the oxidation of a number of alternative aldose sugars, such as D-xylose, D-galactose, and D-fucose, to the corresponding glyconate. Can utilize both NAD(+) and NADP(+) as electron acceptor, with a preference for NADP(+). Physiologically, seems to be involved in the degradation of glucose through a modified Entner-Doudoroff pathway.<ref>PMID:11425479</ref> <ref>PMID:8925901</ref>	+	[[https://www.uniprot.org/uniprot/GLCDH_HALMT GLCDH_HALMT]] Catalyzes the NAD(P)(+)-dependent oxidation of D-glucose to D-gluconate. Displays broad substrate specificity since it is able to catalyze the oxidation of a number of alternative aldose sugars, such as D-xylose, D-galactose, and D-fucose, to the corresponding glyconate. Can utilize both NAD(+) and NADP(+) as electron acceptor, with a preference for NADP(+). Physiologically, seems to be involved in the degradation of glucose through a modified Entner-Doudoroff pathway.<ref>PMID:11425479</ref> <ref>PMID:8925901</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	[[Category: Atcc 33500]]		[[Category: Atcc 33500]]
	[[Category: Glucose 1-dehydrogenase]]		[[Category: Glucose 1-dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Baker, P J]]		[[Category: Baker, P J]]
	[[Category: Bonete, M J]]		[[Category: Bonete, M J]]

OCA at 06:09, 16 May 2018

OCA — Wed, 16 May 2018 06:09:50 GMT

←Older revision		Revision as of 06:09, 16 May 2018
Line 1:		Line 1:
		+
	==Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei==		==Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei==
	<StructureSection load='2b5w' size='340' side='right' caption='[[2b5w]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2b5w' size='340' side='right' caption='[[2b5w]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gdh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 ATCC 33500])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gdh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 ATCC 33500])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [http://pdbe.org/2b5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [http://www.ebi.ac.uk/pdbsum/2b5w 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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [http://pdbe.org/2b5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [http://www.ebi.ac.uk/pdbsum/2b5w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2b5w 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/b5/2b5w_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b5/2b5w_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 01:36, 7 February 2016

OCA — Sun, 07 Feb 2016 01:36:42 GMT

←Older revision		Revision as of 01:36, 7 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=2b5w ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:23, 9 September 2015

OCA — Wed, 09 Sep 2015 20:23:47 GMT

←Older revision		Revision as of 20:23, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='2b5w' size='340' side='right' caption='[[2b5w]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2b5w' size='340' side='right' caption='[[2b5w]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2b5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Haloferax_mediterranei Haloferax mediterranei~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B5W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2b5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_33500 Atcc 33500]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B5W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5v\|2b5v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5v\|2b5v]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gdh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 ~~Haloferax mediterranei~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gdh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 ATCC 33500])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [http://www.ebi.ac.uk/pdbsum/2b5w 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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [http://pdbe.org/2b5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [http://www.ebi.ac.uk/pdbsum/2b5w PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~Q977U7_HALME Q977U7_HALME~~]] Catalyzes the NAD(P)(+)-dependent oxidation of D-glucose to D-gluconate. Displays broad substrate specificity since it is able to catalyze the oxidation of a number of alternative aldose sugars, such as D-xylose, D-galactose, and D-fucose, to the corresponding glyconate. Can utilize both NAD(+) and NADP(+) as electron acceptor, with a preference for NADP(+). Physiologically, seems to be involved in the degradation of glucose through a modified Entner-Doudoroff pathway.<ref>PMID:11425479</ref> <ref>PMID:8925901</ref>	+	[[http://www.uniprot.org/uniprot/GLCDH_HALMT GLCDH_HALMT]] Catalyzes the NAD(P)(+)-dependent oxidation of D-glucose to D-gluconate. Displays broad substrate specificity since it is able to catalyze the oxidation of a number of alternative aldose sugars, such as D-xylose, D-galactose, and D-fucose, to the corresponding glyconate. Can utilize both NAD(+) and NADP(+) as electron acceptor, with a preference for NADP(+). Physiologically, seems to be involved in the degradation of glucose through a modified Entner-Doudoroff pathway.<ref>PMID:11425479</ref> <ref>PMID:8925901</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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 2b5w" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 33500]]
	[[Category: Glucose 1-dehydrogenase]]		[[Category: Glucose 1-dehydrogenase]]
-	[[Category: Haloferax mediterranei]]
	[[Category: Baker, P J]]		[[Category: Baker, P J]]
	[[Category: Bonete, M J]]		[[Category: Bonete, M J]]

OCA at 06:39, 24 December 2014

OCA — Wed, 24 Dec 2014 06:39:42 GMT

←Older revision		Revision as of 06:39, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2b5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloferax_mediterranei Haloferax mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B5W FirstGlance]. <br>		<table><tr><td colspan='2'>[[2b5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloferax_mediterranei Haloferax mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B5W FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5v\|2b5v]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5v\|2b5v]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gdh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 Haloferax mediterranei])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gdh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 Haloferax mediterranei])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [http://www.ebi.ac.uk/pdbsum/2b5w 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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [http://www.ebi.ac.uk/pdbsum/2b5w PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q977U7_HALME Q977U7_HALME]] Catalyzes the NAD(P)(+)-dependent oxidation of D-glucose to D-gluconate. Displays broad substrate specificity since it is able to catalyze the oxidation of a number of alternative aldose sugars, such as D-xylose, D-galactose, and D-fucose, to the corresponding glyconate. Can utilize both NAD(+) and NADP(+) as electron acceptor, with a preference for NADP(+). Physiologically, seems to be involved in the degradation of glucose through a modified Entner-Doudoroff pathway.<ref>PMID:11425479</ref> <ref>PMID:8925901</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Glucose 1-dehydrogenase]]		[[Category: Glucose 1-dehydrogenase]]
	[[Category: Haloferax mediterranei]]		[[Category: Haloferax mediterranei]]
-	[[Category: Baker, P J.]]	+	[[Category: Baker, P J]]
-	[[Category: Bonete, M J.]]	+	[[Category: Bonete, M J]]
-	[[Category: Britton, K L.]]	+	[[Category: Britton, K L]]
-	[[Category: Esclapez, J.]]	+	[[Category: Esclapez, J]]
-	[[Category: Ferrer, J.]]	+	[[Category: Ferrer, J]]
-	[[Category: Fisher, M.]]	+	[[Category: Fisher, M]]
-	[[Category: Gilmour, D J.]]	+	[[Category: Gilmour, D J]]
-	[[Category: Pire, C.]]	+	[[Category: Pire, C]]
-	[[Category: Rice, D W.]]	+	[[Category: Rice, D W]]
-	[[Category: Ruzheinikov, S.]]	+	[[Category: Ruzheinikov, S]]
	[[Category: Nucleotide binding motif]]		[[Category: Nucleotide binding motif]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 23:44, 29 September 2014

OCA — Mon, 29 Sep 2014 23:44:42 GMT

←Older revision		Revision as of 23:44, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2b5w.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei==
		+	<StructureSection load='2b5w' size='340' side='right' caption='[[2b5w]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2b5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloferax_mediterranei Haloferax mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2B5W FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2b5v\|2b5v]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gdh ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2252 Haloferax mediterranei])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucose_1-dehydrogenase Glucose 1-dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.47 1.1.1.47] </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=2b5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b5w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2b5w RCSB], [http://www.ebi.ac.uk/pdbsum/2b5w 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/b5/2b5w_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 glucose dehydrogenase from the extreme halophile Haloferax mediterranei has been solved at 1.6-A resolution under crystallization conditions which closely mimic the "in vivo" intracellular environment. The decoration of the enzyme's surface with acidic residues is only partially neutralized by bound potassium counterions, which also appear to play a role in substrate binding. The surface shows the expected reduction in hydrophobic character, surprisingly not from changes associated with the loss of exposed hydrophobic residues but rather arising from a loss of lysines consistent with the genome wide-reduction of this residue in extreme halophiles. The structure reveals a highly ordered, multilayered solvation shell that can be seen to be organized into one dominant network covering much of the exposed surface accessible area to an extent not seen in almost any other protein structure solved. This finding is consistent with the requirement of the enzyme to form a protective shell in a dehydrating environment.

-	~~{{STRUCTURE_2b5w\| PDB=2b5w \| SCENE= }}~~	+	Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei.,Britton KL, Baker PJ, Fisher M, Ruzheinikov S, Gilmour DJ, Bonete MJ, Ferrer J, Pire C, Esclapez J, Rice DW Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):4846-51. Epub 2006 Mar 21. PMID:16551747<ref>PMID:16551747</ref>

-	~~===Crystal structure~~ of ~~D38C glucose dehydrogenase mutant from Haloferax mediterranei===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16551747}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2b5w]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Haloferax_mediterranei Haloferax mediterranei]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016551747<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Glucose 1-dehydrogenase]]		[[Category: Glucose 1-dehydrogenase]]
	[[Category: Haloferax mediterranei]]		[[Category: Haloferax mediterranei]]

OCA at 12:11, 23 January 2013

OCA — Wed, 23 Jan 2013 12:11:41 GMT

←Older revision		Revision as of 12:11, 23 January 2013
Line 1:		Line 1:
	[[Image:2b5w.png\|left\|200px]]		[[Image:2b5w.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2b5w", 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_2b5w\| PDB=2b5w \| SCENE= }}		{{STRUCTURE_2b5w\| PDB=2b5w \| SCENE= }}

	===Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei===		===Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16551747}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16551747 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16551747}}		{{ABSTRACT_PUBMED_16551747}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16551747</ref><ref group="xtra">PMID:11717506~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016551747</ref><references group="xtra"/>
	[[Category: Glucose 1-dehydrogenase]]		[[Category: Glucose 1-dehydrogenase]]
	[[Category: Haloferax mediterranei]]		[[Category: Haloferax mediterranei]]

OCA: Protected "2b5w" [edit=sysop:move=sysop]

OCA — Mon, 14 Mar 2011 12:35:52 GMT

Protected "2b5w" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:35, 14 March 2011

OCA at 12:35, 14 March 2011

OCA — Mon, 14 Mar 2011 12:35:51 GMT

←Older revision		Revision as of 12:35, 14 March 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2b5w.png\|left\|200px]]		[[Image:2b5w.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~2B5W~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Haloferax_mediterranei Haloferax mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA].	+	[[2b5w]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloferax_mediterranei Haloferax mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B5W OCA].

	==Reference==		==Reference==
Line 37:		Line 36:
	[[Category: Ruzheinikov, S.]]		[[Category: Ruzheinikov, S.]]
	[[Category: Nucleotide binding motif]]		[[Category: Nucleotide binding motif]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 09:49:27 2009''~~	+