5ilo - Revision history

OCA at 14:00, 30 August 2023

2023-08-30T14:00:39Z

← Older revision		Revision as of 14:00, 30 August 2023
Line 1:		Line 1:

	==Crystal structure of photoreceptor dehydrogenase from Drosophila melanogaster==		==Crystal structure of photoreceptor dehydrogenase from Drosophila melanogaster==
	<StructureSection load='5ilo' size='340' side='right' caption='[[5ilo]], [[Resolution\|resolution]] 2.71Å' scene=''>		<StructureSection load='5ilo' size='340' side='right'caption='[[5ilo]], [[Resolution\|resolution]] 2.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ilo]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ILO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ILO FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ilo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ILO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ILO 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>~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.71Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5ilg\|5ilg]]</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></td></tr>
	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></~~td><td class="sblockDat"~~>~~Pdh, pcdr, CG4899, Dmel_CG4899 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])~~</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=5ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ilo OCA], [https://pdbe.org/5ilo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ilo RCSB], [https://www.ebi.ac.uk/pdbsum/5ilo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ilo ProSAT]</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=5ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ilo OCA], [~~http~~://pdbe.org/5ilo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ilo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ilo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ilo ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q9VV42_DROME Q9VV42_DROME]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Drome~~]]		[[Category: Drosophila melanogaster]]
	[[Category: ~~Banerjee, S~~]]		[[Category: Large Structures]]
	[[Category: ~~Hofmann, L~~]]		[[Category: Banerjee S]]
	[[Category: ~~Tsybovsky, Y~~]]		[[Category: Hofmann L]]
	[[Category: ~~Oxidoreductase]]~~		[[Category: Tsybovsky Y]]
	~~[[Category: Short-chain dehydrogenase~~]]

OCA at 05:47, 25 April 2018

2018-04-25T05:47:54Z

← Older revision		Revision as of 05:47, 25 April 2018
Line 3:		Line 3:
	<StructureSection load='5ilo' size='340' side='right' caption='[[5ilo]], [[Resolution\|resolution]] 2.71Å' scene=''>		<StructureSection load='5ilo' size='340' side='right' caption='[[5ilo]], [[Resolution\|resolution]] 2.71Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ilo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ILO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ILO FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ilo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ILO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ILO 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ilg\|5ilg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ilg\|5ilg]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Pdh, pcdr, CG4899, Dmel_CG4899 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=5ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ilo OCA], [http://pdbe.org/5ilo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ilo RCSB], [http://www.ebi.ac.uk/pdbsum/5ilo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ilo ProSAT]</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=5ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ilo OCA], [http://pdbe.org/5ilo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ilo RCSB], [http://www.ebi.ac.uk/pdbsum/5ilo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ilo ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The 11-cis-retinylidene chromophore of visual pigments isomerizes upon interaction with a photon, initiating a downstream cascade of signaling events that ultimately lead to visual perception. 11-cis-Retinylidene is regenerated through enzymatic transformations collectively called the visual cycle. The first and rate-limiting enzymatic reaction within this cycle, i.e., the reduction of all-trans-retinal to all-trans-retinol, is catalyzed by retinol dehydrogenases. Here, we determined the structure of Drosophila melanogaster photoreceptor retinol dehydrogenase (PDH) isoform C that belongs to the short-chain dehydrogenase/reductase (SDR) family. This is the first reported structure of a SDR that possesses this biologically important activity. Two crystal structures of the same enzyme grown under different conditions revealed a novel conformational change of the NAD(+) cofactor, likely representing a change during catalysis. Amide hydrogen-deuterium exchange of PDH demonstrated changes in the structure of the enzyme upon dinucleotide binding. In D. melanogaster, loss of PDH activity leads to photoreceptor degeneration that can be partially rescued by transgenic expression of human RDH12. Based on the structure of PDH, we analyzed mutations causing Leber congenital amaurosis 13 in a homology model of human RDH12 to obtain insights into the molecular basis of RDH12 disease-causing mutations.

			Structural Insights into the Drosophila melanogaster Retinol Dehydrogenase, a Member of the Short-Chain Dehydrogenase/Reductase Family.,Hofmann L, Tsybovsky Y, Alexander NS, Babino D, Leung NY, Montell C, Banerjee S, von Lintig J, Palczewski K Biochemistry. 2016 Nov 29;55(47):6545-6557. doi: 10.1021/acs.biochem.6b00907., Epub 2016 Nov 16. PMID:27809489<ref>PMID:27809489</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 5ilo" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Drome]]
	[[Category: Banerjee, S]]		[[Category: Banerjee, S]]
	[[Category: Hofmann, L]]		[[Category: Hofmann, L]]

OCA at 03:27, 10 December 2016

2016-12-10T03:27:16Z

← Older revision		Revision as of 03:27, 10 December 2016
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 5ilo is ~~ON HOLD until Paper Publication~~		==Crystal structure of photoreceptor dehydrogenase from Drosophila melanogaster==
			<StructureSection load='5ilo' size='340' side='right' caption='[[5ilo]], [[Resolution\|resolution]] 2.71Å' scene=''>
	~~Authors~~: ~~Hofmann~~, L., ~~Tsybovsky~~, Y., ~~Banerjee~~, S.		== Structural highlights ==
			<table><tr><td colspan='2'>[[5ilo]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ILO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ILO FirstGlance]. <br>
	~~Description: Crystal structure of photoreceptor dehydrogenase from Drosophila melanogaster~~		</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></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ilg\|5ilg]]</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=5ilo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ilo OCA], [http://pdbe.org/5ilo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ilo RCSB], [http://www.ebi.ac.uk/pdbsum/5ilo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ilo ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Banerjee, S]]
	[[Category: Hofmann, L]]		[[Category: Hofmann, L]]
	~~[[Category: Banerjee, S]]~~
	[[Category: Tsybovsky, Y]]		[[Category: Tsybovsky, Y]]
			[[Category: Oxidoreductase]]
			[[Category: Short-chain dehydrogenase]]

OCA: Protected "5ilo" [edit=sysop:move=sysop]

2016-05-11T00:37:25Z

Protected "5ilo" [edit=sysop:move=sysop]

← Older revision	Revision as of 00:37, 11 May 2016
(No difference)

OCA: New page: '''Unreleased structure''' The entry 5ilo is ON HOLD until Paper Publication Authors: Hofmann, L., Tsybovsky, Y., Banerjee, S. Description: Crystal structure of photoreceptor dehydroge...

2016-05-11T00:37:24Z

New page: '''Unreleased structure''' The entry 5ilo is ON HOLD until Paper Publication Authors: Hofmann, L., Tsybovsky, Y., Banerjee, S. Description: Crystal structure of photoreceptor dehydroge...

New page

'''Unreleased structure'''

The entry 5ilo is ON HOLD until Paper Publication

Authors: Hofmann, L., Tsybovsky, Y., Banerjee, S.

Description: Crystal structure of photoreceptor dehydrogenase from Drosophila melanogaster
[[Category: Unreleased Structures]]
[[Category: Hofmann, L]]
[[Category: Banerjee, S]]
[[Category: Tsybovsky, Y]]