1lc3 - Revision history

OCA at 07:31, 14 February 2024

2024-02-14T07:31:50Z

←Older revision		Revision as of 07:31, 14 February 2024
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	<StructureSection load='1lc3' size='340' side='right'caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1lc3' size='340' side='right'caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1lc0\|1lc0]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24]~~ </~~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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [https://pdbe.org/1lc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [https://www.ebi.ac.uk/pdbsum/1lc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lc3 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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [https://pdbe.org/1lc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [https://www.ebi.ac.uk/pdbsum/1lc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lc3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BIEA_RAT BIEA_RAT]] Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor.	+	[https://www.uniprot.org/uniprot/BIEA_RAT BIEA_RAT] Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor.
	== 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=1lc3 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=1lc3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Biliverdin reductase (BVR) catalyzes the last step in heme degradation by reducing the gamma-methene bridge of the open tetrapyrrole, biliverdin IXalpha, to bilirubin with the concomitant oxidation of a beta-nicotinamide adenine dinucleotide (NADH) or beta-nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. Bilirubin is the major bile pigment in mammals and has antioxidant and anticompliment activity. We have determined X-ray crystal structures of apo rat BVR and its complex with NADH at 1.2 A and 1.5 A resolution, respectively. In agreement with an independent structure determination of the apo-enzyme, BVR consists of an N-terminal dinucleotide-binding domain (Rossmann-fold) and a C-terminal domain that contains a six-stranded beta-sheet that is flanked on one face by several alpha-helices. The C-terminal and N-terminal domains interact extensively, forming the active site cleft at their interface. The cofactor complex structure reported here reveals that the cofactor nicotinamide ring extends into the active site cleft, where it is adjacent to conserved amino acid residues and, consistent with the known stereochemistry of the reaction catalyzed by BVR, the si face of the ring is accessible for hydride transfer. The only titratable side-chain that appears to be suitably positioned to function as a general acid in catalysis is Tyr97. This residue, however, is not essential for catalysis, since the Tyr97Phe mutant protein retains 50% activity. This finding suggests that the dominant role in catalysis may be performed by hydride transfer from the cofactor, a process that may be promoted by proximity of the invariant residues Glu96, Glu123, and Glu126, to the nicotinamide ring.
-
-	Crystal structure of a biliverdin IXalpha reductase enzyme-cofactor complex.,Whitby FG, Phillips JD, Hill CP, McCoubrey W, Maines MD J Mol Biol. 2002 Jun 21;319(5):1199-210. PMID:12079357<ref>PMID:12079357</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1lc3" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Biliverdin reductase]]
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Hill, C P~~]]	+	[[Category: Rattus norvegicus]]
-	[[Category: ~~Maines, M D~~]]	+	[[Category: Hill CP]]
-	[[Category: ~~McCoubrey, W~~]]	+	[[Category: Maines MD]]
-	[[Category: ~~Phillips, J D~~]]	+	[[Category: McCoubrey W]]
-	[[Category: ~~Whitby, F G~~]]	+	[[Category: Phillips JD]]
-	[[Category: ~~Bile pigment]]~~	+	[[Category: Whitby FG]]
-	~~[[Category: Bilirubin]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Nadh]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Tetrapyrrole~~]]	+

OCA at 06:42, 18 August 2021

2021-08-18T06:42:25Z

←Older revision		Revision as of 06:42, 18 August 2021
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	<StructureSection load='1lc3' size='340' side='right'caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1lc3' size='340' side='right'caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lc0\|1lc0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lc0\|1lc0]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24] </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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [~~http~~://pdbe.org/1lc3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lc3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lc3 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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [https://pdbe.org/1lc3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [https://www.ebi.ac.uk/pdbsum/1lc3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lc3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BIEA_RAT BIEA_RAT]] Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor.	+	[[https://www.uniprot.org/uniprot/BIEA_RAT BIEA_RAT]] Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:32, 13 November 2019

2019-11-13T12:32:45Z

←Older revision		Revision as of 12:32, 13 November 2019
Line 1:		Line 1:

	==Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex==		==Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex==
-	<StructureSection load='1lc3' size='340' side='right' caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='1lc3' size='340' side='right'caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>
Line 36:		Line 36:
	[[Category: Biliverdin reductase]]		[[Category: Biliverdin reductase]]
	[[Category: Buffalo rat]]		[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Hill, C P]]		[[Category: Hill, C P]]
	[[Category: Maines, M D]]		[[Category: Maines, M D]]

OCA at 21:43, 24 January 2018

2018-01-24T21:43:06Z

←Older revision		Revision as of 21:43, 24 January 2018
Line 1:		Line 1:
		+
	==Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex==		==Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex==
	<StructureSection load='1lc3' size='340' side='right' caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1lc3' size='340' side='right' caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lc0\|1lc0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lc0\|1lc0]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24] </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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [http://pdbe.org/1lc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [http://www.ebi.ac.uk/pdbsum/1lc3 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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [http://pdbe.org/1lc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [http://www.ebi.ac.uk/pdbsum/1lc3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lc3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lc/1lc3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lc/1lc3_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 08:23, 8 February 2016

2016-02-08T08:23:15Z

←Older revision		Revision as of 08:23, 8 February 2016
Line 18:		Line 18:
	<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=1lc3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:40, 10 September 2015

2015-09-10T09:40:35Z

←Older revision		Revision as of 09:40, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1lc3' size='340' side='right' caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='1lc3' size='340' side='right' caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rattus_norvegicus Rattus norvegicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lc0\|1lc0]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lc0\|1lc0]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24] </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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [http://www.ebi.ac.uk/pdbsum/1lc3 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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [http://pdbe.org/1lc3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [http://www.ebi.ac.uk/pdbsum/1lc3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1lc3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Biliverdin reductase]]		[[Category: Biliverdin reductase]]
-	[[Category: ~~Rattus norvegicus~~]]	+	[[Category: Buffalo rat]]
	[[Category: Hill, C P]]		[[Category: Hill, C P]]
	[[Category: Maines, M D]]		[[Category: Maines, M D]]

OCA at 21:56, 24 December 2014

2014-12-24T21:56:30Z

←Older revision		Revision as of 21:56, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lc0\|1lc0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lc0\|1lc0]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24] </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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [http://www.ebi.ac.uk/pdbsum/1lc3 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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [http://www.ebi.ac.uk/pdbsum/1lc3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BIEA_RAT BIEA_RAT]] Reduces the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Biliverdin reductase]]		[[Category: Biliverdin reductase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
-	[[Category: Hill, C P.]]	+	[[Category: Hill, C P]]
-	[[Category: Maines, M D.]]	+	[[Category: Maines, M D]]
-	[[Category: McCoubrey, W.]]	+	[[Category: McCoubrey, W]]
-	[[Category: Phillips, J D.]]	+	[[Category: Phillips, J D]]
-	[[Category: Whitby, F G.]]	+	[[Category: Whitby, F G]]
	[[Category: Bile pigment]]		[[Category: Bile pigment]]
	[[Category: Bilirubin]]		[[Category: Bilirubin]]
-	[[Category: Biliverdin reductase]]
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Nadh]]		[[Category: Nadh]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Tetrapyrrole]]		[[Category: Tetrapyrrole]]

OCA at 18:31, 28 September 2014

2014-09-28T18:31:53Z

←Older revision		Revision as of 18:31, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1lc3.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex==
		+	<StructureSection load='1lc3' size='340' side='right' caption='[[1lc3]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1lc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LC3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lc0\|1lc0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biliverdin_reductase Biliverdin reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.24 1.3.1.24] </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=1lc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lc3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lc3 RCSB], [http://www.ebi.ac.uk/pdbsum/1lc3 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/lc/1lc3_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 ==
		+	Biliverdin reductase (BVR) catalyzes the last step in heme degradation by reducing the gamma-methene bridge of the open tetrapyrrole, biliverdin IXalpha, to bilirubin with the concomitant oxidation of a beta-nicotinamide adenine dinucleotide (NADH) or beta-nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. Bilirubin is the major bile pigment in mammals and has antioxidant and anticompliment activity. We have determined X-ray crystal structures of apo rat BVR and its complex with NADH at 1.2 A and 1.5 A resolution, respectively. In agreement with an independent structure determination of the apo-enzyme, BVR consists of an N-terminal dinucleotide-binding domain (Rossmann-fold) and a C-terminal domain that contains a six-stranded beta-sheet that is flanked on one face by several alpha-helices. The C-terminal and N-terminal domains interact extensively, forming the active site cleft at their interface. The cofactor complex structure reported here reveals that the cofactor nicotinamide ring extends into the active site cleft, where it is adjacent to conserved amino acid residues and, consistent with the known stereochemistry of the reaction catalyzed by BVR, the si face of the ring is accessible for hydride transfer. The only titratable side-chain that appears to be suitably positioned to function as a general acid in catalysis is Tyr97. This residue, however, is not essential for catalysis, since the Tyr97Phe mutant protein retains 50% activity. This finding suggests that the dominant role in catalysis may be performed by hydride transfer from the cofactor, a process that may be promoted by proximity of the invariant residues Glu96, Glu123, and Glu126, to the nicotinamide ring.

-	~~{{STRUCTURE_1lc3\| PDB=1lc3 \| SCENE= }}~~	+	Crystal structure of a biliverdin IXalpha reductase enzyme-cofactor complex.,Whitby FG, Phillips JD, Hill CP, McCoubrey W, Maines MD J Mol Biol. 2002 Jun 21;319(5):1199-210. PMID:12079357<ref>PMID:12079357</ref>

-	~~===Crystal Structure~~ of ~~a Biliverdin Reductase Enzyme-Cofactor Complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12079357}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1lc3]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Rattus_norvegicus Rattus norvegicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012079357<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Biliverdin reductase]]		[[Category: Biliverdin reductase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]

OCA: Protected "1lc3" [edit=sysop:move=sysop]

2012-12-05T21:18:25Z

Protected "1lc3" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:18, 5 December 2012

OCA at 21:18, 5 December 2012

2012-12-05T21:18:23Z

←Older revision		Revision as of 21:18, 5 December 2012
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-	{{Seed}}
	[[Image:1lc3.png\|left\|200px]]		[[Image:1lc3.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_1lc3\| PDB=1lc3 \| SCENE= }}		{{STRUCTURE_1lc3\| PDB=1lc3 \| SCENE= }}

	===Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex===		===Crystal Structure of a Biliverdin Reductase Enzyme-Cofactor Complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12079357}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12079357 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_12079357}}		{{ABSTRACT_PUBMED_12079357}}

	==About this Structure==		==About this Structure==
-	~~1LC3~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA].	+	[[1lc3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LC3 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12079357~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012079357</ref><references group="xtra"/>
	[[Category: Biliverdin reductase]]		[[Category: Biliverdin reductase]]
	[[Category: Rattus norvegicus]]		[[Category: Rattus norvegicus]]
Line 36:		Line 24:
	[[Category: Heme]]		[[Category: Heme]]
	[[Category: Nadh]]		[[Category: Nadh]]
		+	[[Category: Oxidoreductase]]
	[[Category: Tetrapyrrole]]		[[Category: Tetrapyrrole]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:33:27 2009''