5dbi - Revision history

OCA at 16:15, 8 November 2023

2023-11-08T16:15:32Z

←Older revision		Revision as of 16:15, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5dbi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Catharanthus_roseus Catharanthus roseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DBI FirstGlance]. <br>		<table><tr><td colspan='2'>[[5dbi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Catharanthus_roseus Catharanthus roseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DBI 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=XOG:(2E,6E)-2,6-DIMETHYLOCTA-2,6-DIENEDIAL'>XOG</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]] 2.2Å</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=XOG:(2E,6E)-2,6-DIMETHYLOCTA-2,6-DIENEDIAL'>XOG</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=5dbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbi OCA], [https://pdbe.org/5dbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dbi RCSB], [https://www.ebi.ac.uk/pdbsum/5dbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbi 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=5dbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbi OCA], [https://pdbe.org/5dbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dbi RCSB], [https://www.ebi.ac.uk/pdbsum/5dbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbi ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:29, 21 June 2023

2023-06-21T10:29:22Z

←Older revision		Revision as of 10:29, 21 June 2023
Line 3:		Line 3:
	<StructureSection load='5dbi' size='340' side='right'caption='[[5dbi]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5dbi' size='340' side='right'caption='[[5dbi]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dbi]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Catro Catro~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5DBI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dbi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Catharanthus_roseus Catharanthus roseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DBI 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=XOG:(2E,6E)-2,6-DIMETHYLOCTA-2,6-DIENEDIAL'>XOG</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=XOG:(2E,6E)-2,6-DIMETHYLOCTA-2,6-DIENEDIAL'>XOG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dbf\|5dbf]], [[5dbg\|5dbg]]</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=5dbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbi OCA], [https://pdbe.org/5dbi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dbi RCSB], [https://www.ebi.ac.uk/pdbsum/5dbi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbi ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Iridoid_synthase Iridoid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.99 1.3.1.99] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5dbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbi OCA], [~~http~~://pdbe.org/5dbi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5dbi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5dbi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbi ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/IRIS_CATRO IRIS_CATRO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Catro]]~~	+	[[Category: Catharanthus roseus]]
-	~~[[Category: Iridoid synthase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chen~~, C C~~]]	+	[[Category: Chen CC]]
-	[[Category: Guo~~, R T~~]]	+	[[Category: Guo RT]]
-	[[Category: Hu~~, Y M~~]]	+	[[Category: Hu YM]]
-	[[Category: Ko~~, T P~~]]	+	[[Category: Ko TP]]
-	[[Category: Liu~~, W D~~]]	+	[[Category: Liu WD]]
-	[[Category: Xu~~, Z X~~]]	+	[[Category: Xu ZX]]
-	[[Category: Zheng~~, Y Y]]~~	+	[[Category: Zheng YY]]
-	~~[[Category: Acidocalcisomal pyrophosphatase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Substrate binding~~]]	+

OCA at 07:58, 8 April 2020

2020-04-08T07:58:23Z

←Older revision		Revision as of 07:58, 8 April 2020
Line 1:		Line 1:
		+
	==Crystal Structure of Iridoid Synthase from Cantharanthus roseus in complex with NAD+ and 10-oxogeranial==		==Crystal Structure of Iridoid Synthase from Cantharanthus roseus in complex with NAD+ and 10-oxogeranial==
-	<StructureSection load='5dbi' size='340' side='right' caption='[[5dbi]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5dbi' size='340' side='right'caption='[[5dbi]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5dbi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DBI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5dbi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Catro Catro]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DBI 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=XOG:(2E,6E)-2,6-DIMETHYLOCTA-2,6-DIENEDIAL'>XOG</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=XOG:(2E,6E)-2,6-DIMETHYLOCTA-2,6-DIENEDIAL'>XOG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dbf\|5dbf]], [[5dbg\|5dbg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dbf\|5dbf]], [[5dbg\|5dbg]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Iridoid_synthase Iridoid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.99 1.3.1.99] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Iridoid_synthase Iridoid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.99 1.3.1.99] </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=5dbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbi OCA], [http://pdbe.org/5dbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dbi RCSB], [http://www.ebi.ac.uk/pdbsum/5dbi PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5dbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbi OCA], [http://pdbe.org/5dbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dbi RCSB], [http://www.ebi.ac.uk/pdbsum/5dbi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dbi ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Catro]]
	[[Category: Iridoid synthase]]		[[Category: Iridoid synthase]]
		+	[[Category: Large Structures]]
	[[Category: Chen, C C]]		[[Category: Chen, C C]]
	[[Category: Guo, R T]]		[[Category: Guo, R T]]

OCA at 18:19, 27 January 2016

2016-01-27T18:19:56Z

←Older revision		Revision as of 18:19, 27 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal Structure of Iridoid Synthase from Cantharanthus roseus in complex with NAD+ and 10-oxogeranial==
		+	<StructureSection load='5dbi' size='340' side='right' caption='[[5dbi]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5dbi]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DBI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DBI 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=XOG:(2E,6E)-2,6-DIMETHYLOCTA-2,6-DIENEDIAL'>XOG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5dbf\|5dbf]], [[5dbg\|5dbg]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Iridoid_synthase Iridoid synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.99 1.3.1.99] </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=5dbi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dbi OCA], [http://pdbe.org/5dbi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dbi RCSB], [http://www.ebi.ac.uk/pdbsum/5dbi PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Structures of the iridoid synthase nepetalactol synthase in the presence of NAD(+) , NADPH or NAD(+) /10-oxogeranial were solved. The 10-oxogeranial substrate binds in a transoid-O1-C3 conformation and can be reduced by hydride addition to form the byproduct S-10-oxo-citronellal. Tyr178 Ozeta is positioned 2.5 A from the substrate O1 and provides the second proton required for reaction. Nepetalactol product formation requires rotation about C1-C2 to form the cisoid isomer, leading to formation of the cis-enolate, together with rotation about C4-C5, which enables cyclization and lactol production. The structure is similar to that of progesterone-5beta-reductase, with almost identical positioning of NADP, Lys146(147), Tyr178(179), and F342(343), but only Tyr178 and Phe342 appear to be essential for activity. The transoid 10-oxogeranial structure also serves as a model for beta-face hydride attack in progesterone 5beta-reductases and is of general interest in the context of asymmetric synthesis.

-	~~The entry 5dbi is ON HOLD until Aug 21 2017~~	+	Structures of Iridoid Synthase from Cantharanthus roseus with Bound NAD(+) , NADPH, or NAD(+) /10-Oxogeranial: Reaction Mechanisms.,Hu Y, Liu W, Malwal SR, Zheng Y, Feng X, Ko TP, Chen CC, Xu Z, Liu M, Han X, Gao J, Oldfield E, Guo RT Angew Chem Int Ed Engl. 2015 Dec 14;54(51):15478-82. doi: 10.1002/anie.201508310., Epub 2015 Nov 13. PMID:26768532<ref>PMID:26768532</ref>

-	~~Authors: Hu~~, Y.M.~~, Liu, W.D., Zheng, Y.Y., Xu, Z.X., Ko, T.P., Chen, C.C., Guo, R.T~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of reductase in complex with NAD and substrate~~	+	<div class="pdbe-citations 5dbi" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: Ko, ~~T.P~~]]	+	<references/>
-	[[Category: ~~Chen~~, ~~C.C~~]]	+	__TOC__
-	[[Category: Hu, Y.M]]	+	</StructureSection>
-	[[Category: Liu, W.D]]	+	[[Category: Iridoid synthase]]
-	[[Category: Xu, Z.X]]	+	[[Category: Chen, C C]]
-	[[Category: ~~Guo~~, ~~R.T~~]]	+	[[Category: Guo, R T]]
-	[[Category: ~~Zheng, Y.Y~~]]	+	[[Category: Hu, Y M]]
		+	[[Category: Ko, T P]]
		+	[[Category: Liu, W D]]
		+	[[Category: Xu, Z X]]
		+	[[Category: Zheng, Y Y]]
		+	[[Category: Acidocalcisomal pyrophosphatase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Metal-binding]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Substrate binding]]

OCA at 10:00, 9 September 2015

2015-09-09T10:00:35Z

←Older revision		Revision as of 10:00, 9 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5dbi is ON HOLD	+	The entry 5dbi is ON HOLD until Aug 21 2017

	Authors: Hu, Y.M., Liu, W.D., Zheng, Y.Y., Xu, Z.X., Ko, T.P., Chen, C.C., Guo, R.T.		Authors: Hu, Y.M., Liu, W.D., Zheng, Y.Y., Xu, Z.X., Ko, T.P., Chen, C.C., Guo, R.T.

-	Description: Crystal structure of reductase in complex with NAD and substrate ~~from Catharanthus roseus~~	+	Description: Crystal structure of reductase in complex with NAD and substrate
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Ko, T.P]]		[[Category: Ko, T.P]]

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

2015-08-26T12:42:54Z

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

←Older revision

Revision as of 12:42, 26 August 2015

OCA: New page: '''Unreleased structure''' The entry 5dbi is ON HOLD Authors: Hu, Y.M., Liu, W.D., Zheng, Y.Y., Xu, Z.X., Ko, T.P., Chen, C.C., Guo, R.T. Description: Crystal structure of reductase in...

2015-08-26T12:42:53Z

New page: '''Unreleased structure''' The entry 5dbi is ON HOLD Authors: Hu, Y.M., Liu, W.D., Zheng, Y.Y., Xu, Z.X., Ko, T.P., Chen, C.C., Guo, R.T. Description: Crystal structure of reductase in...

New page

'''Unreleased structure'''

The entry 5dbi is ON HOLD

Authors: Hu, Y.M., Liu, W.D., Zheng, Y.Y., Xu, Z.X., Ko, T.P., Chen, C.C., Guo, R.T.

Description: Crystal structure of reductase in complex with NAD and substrate from Catharanthus roseus
[[Category: Unreleased Structures]]
[[Category: Ko, T.P]]
[[Category: Chen, C.C]]
[[Category: Hu, Y.M]]
[[Category: Liu, W.D]]
[[Category: Xu, Z.X]]
[[Category: Guo, R.T]]
[[Category: Zheng, Y.Y]]