4ln9 - Revision history

OCA at 16:21, 20 September 2023

OCA — Wed, 20 Sep 2023 16:21:45 GMT

←Older revision		Revision as of 16:21, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ln9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_mediterranei Amycolatopsis mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LN9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ln9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_mediterranei Amycolatopsis mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LN9 FirstGlance]. <br>
-	</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=4ln9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ln9 OCA], [https://pdbe.org/4ln9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ln9 RCSB], [https://www.ebi.ac.uk/pdbsum/4ln9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ln9 ProSAT]</span></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]] 1.82Å</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=4ln9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ln9 OCA], [https://pdbe.org/4ln9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ln9 RCSB], [https://www.ebi.ac.uk/pdbsum/4ln9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ln9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 11:13, 14 December 2022

OCA — Wed, 14 Dec 2022 11:13:15 GMT

←Older revision		Revision as of 11:13, 14 December 2022
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	==Crystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase==		==Crystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase==
-	<StructureSection load='4ln9' size='340' side='right' caption='[[4ln9]], [[Resolution\|resolution]] 1.82Å' scene=''>	+	<StructureSection load='4ln9' size='340' side='right'caption='[[4ln9]], [[Resolution\|resolution]] 1.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ln9]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"streptomyces_mediterranei"_margalith_and_beretta_1960 "streptomyces~~ mediterranei~~" margalith and beretta 1960~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LN9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4LN9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ln9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_mediterranei Amycolatopsis mediterranei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LN9 FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3el6\|3el6]], [[3kg6\|3kg6]], [[3kg7\|3kg7]], [[3kg8\|3kg8]], [[3kg9\|3kg9]]</td></tr>~~	+	</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=4ln9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ln9 OCA], [https://pdbe.org/4ln9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ln9 RCSB], [https://www.ebi.ac.uk/pdbsum/4ln9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ln9 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rifE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33910 "Streptomyces mediterranei" Margalith and Beretta 1960])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </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=4ln9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ln9 OCA], [~~http~~://pdbe.org/4ln9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ln9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ln9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ln9 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O54593_AMYMD O54593_AMYMD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Streptomyces~~ mediterranei ~~margalith and beretta 1960~~]]	+	[[Category: Amycolatopsis mediterranei]]
-	[[Category: ~~6-deoxyerythronolide-B synthase~~]]	+	[[Category: Large Structures]]
-	[[Category: Cane, D]]	+	[[Category: Cane D]]
-	[[Category: Gay~~, D C~~]]	+	[[Category: Gay DC]]
-	[[Category: Keatinge-Clay~~, A T~~]]	+	[[Category: Keatinge-Clay AT]]
-	[[Category: You, Y O]]	+	[[Category: You Y-O]]
-	~~[[Category: Dehydration of polyketide intermediate]]~~	+
-	~~[[Category: Double hotdog fold]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Module 10 of rifamycin polyketide synthase~~]]	+

OCA at 16:57, 11 August 2016

OCA — Thu, 11 Aug 2016 16:57:58 GMT

←Older revision		Revision as of 16:57, 11 August 2016
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		+
	==Crystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase==		==Crystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase==
	<StructureSection load='4ln9' size='340' side='right' caption='[[4ln9]], [[Resolution\|resolution]] 1.82Å' scene=''>		<StructureSection load='4ln9' size='340' side='right' caption='[[4ln9]], [[Resolution\|resolution]] 1.82Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rifE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33910 "Streptomyces mediterranei" Margalith and Beretta 1960])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rifE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33910 "Streptomyces mediterranei" Margalith and Beretta 1960])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </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=4ln9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ln9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ln9 RCSB], [http://www.ebi.ac.uk/pdbsum/4ln9 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=4ln9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ln9 OCA], [http://pdbe.org/4ln9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ln9 RCSB], [http://www.ebi.ac.uk/pdbsum/4ln9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ln9 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 4ln9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:22, 5 January 2015

OCA — Mon, 05 Jan 2015 14:22:52 GMT

←Older revision		Revision as of 14:22, 5 January 2015
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-	~~{{STRUCTURE_4ln9\| PDB=4ln9 \| SCENE= }}~~	+	==Crystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase==
-	===Crystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase===	+	<StructureSection load='4ln9' size='340' side='right' caption='[[4ln9]], [[Resolution\|resolution]] 1.82Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24274103}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ln9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_mediterranei"_margalith_and_beretta_1960 "streptomyces mediterranei" margalith and beretta 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LN9 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3el6\|3el6]], [[3kg6\|3kg6]], [[3kg7\|3kg7]], [[3kg8\|3kg8]], [[3kg9\|3kg9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rifE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33910 "Streptomyces mediterranei" Margalith and Beretta 1960])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-deoxyerythronolide-B_synthase 6-deoxyerythronolide-B synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.94 2.3.1.94] </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=4ln9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ln9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ln9 RCSB], [http://www.ebi.ac.uk/pdbsum/4ln9 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RifDH10, the dehydratase domain from the terminal module of the rifamycin polyketide synthase, catalyzes the stereospecific syn dehydration of the model substrate (2S,3S)-2-methyl-3-hydroxypentanoyl-RifACP10, resulting in the exclusive formation of (E)-2-methyl-2-pentenoyl-RifACP10. RifDH10 does not dehydrate any of the other three diastereomeric, RifACP10-bound, diketide thioester substrates. On the other hand, when EryACP6, from the sixth module of the erythromycin polyketide synthase, is substituted for RifACP10, RifDH10 stereospecifically dehydrates only (2R,3R)-2-methyl-3-hydroxypentanoyl-EryACP6 to give exclusively (E)-2-methyl-2-pentenoyl-EryACP6, with no detectable dehydration of any of the other three diastereomeric, EryACP6-bound, diketides. An identical alteration in substrate diastereospecificity was observed for the corresponding N-acetylcysteamine or pantetheine thioester analogues, regardless of acyl chain length or substitution pattern. Incubation of (2RS)-2-methyl-3-ketopentanoyl-RifACP10 with the didomain reductase-dehydratase RifKR10-RifDH10 yielded (E)-2-methyl-2-pentenoyl-RifACP10, the expected product of syn dehydration of (2S,3S)-2-methyl-3-hydroxypentanoyl-RifACP10, while incubation with the corresponding EryACP6-bound substrate, (2RS)-2-methyl-3-ketopentanoyl-EryACP6, gave only the reduction product (2S,3S)-2-methyl-3-hydroxypentanoyl-EryACP6 with no detectable dehydration. These results establish the intrinsic syn dehydration stereochemistry and substrate diastereoselectivity of RifDH10 and highlight the critical role of the natural RifACP10 domain in chaperoning the proper recognition and processing of the natural ACP-bound undecaketide substrate. The 1.82 A resolution structure of RifDH10 reveals the atomic-resolution details of the active site and allows modeling of the syn dehydration of the (2S,3S)-2-methyl-3-hydroxyacyl-RifACP10 substrate. These results suggest that generation of the characteristic cis double bond of the rifamycins occurs after formation of the full-length RifACP10-bound acyclic trans-unsaturated undecaketide intermediate, most likely during the subsequent macrolactamization catalyzed by the amide synthase RifF.

-	~~==About this~~ Structure==	+	Structure and Stereospecificity of the Dehydratase Domain from the Terminal Module of the Rifamycin Polyketide Synthase.,Gay D, You YO, Keatinge-Clay A, Cane DE Biochemistry. 2013 Nov 25. PMID:24274103<ref>PMID:24274103</ref>
-	~~[[4ln9]] is a 2 chain structure. Full crystallographic information is available~~ from ~~[http://oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=4LN9 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:024274103</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Streptomyces mediterranei margalith and beretta 1960]]
	[[Category: 6-deoxyerythronolide-B synthase]]		[[Category: 6-deoxyerythronolide-B synthase]]
-	[[Category: Cane, D.]]	+	[[Category: Cane, D]]
-	[[Category: Gay, D C.]]	+	[[Category: Gay, D C]]
-	[[Category: Keatinge-Clay, A T.]]	+	[[Category: Keatinge-Clay, A T]]
-	[[Category: You, Y O.]]	+	[[Category: You, Y O]]
	[[Category: Dehydration of polyketide intermediate]]		[[Category: Dehydration of polyketide intermediate]]
	[[Category: Double hotdog fold]]		[[Category: Double hotdog fold]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Module 10 of rifamycin polyketide synthase]]		[[Category: Module 10 of rifamycin polyketide synthase]]

OCA at 10:29, 18 December 2013

OCA — Wed, 18 Dec 2013 10:29:57 GMT

←Older revision		Revision as of 10:29, 18 December 2013
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-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4ln9\| PDB=4ln9 \| SCENE= }}
		+	===Crystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase===
		+	{{ABSTRACT_PUBMED_24274103}}

-	~~The entry~~ 4ln9 is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4ln9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LN9 OCA].

-	~~Authors~~: ~~Gay, D.C., You, Y.~~-~~O.,~~ Cane, D., Keatinge-Clay, A.T.	+	==Reference==
-		+	<ref group="xtra">PMID:024274103</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structure~~ of ~~the dehydratase domain from the terminal module~~ of ~~the~~ rifamycin polyketide synthase	+	[[Category: 6-deoxyerythronolide-B synthase]]
		+	[[Category: Cane, D.]]
		+	[[Category: Gay, D C.]]
		+	[[Category: Keatinge-Clay, A T.]]
		+	[[Category: You, Y O.]]
		+	[[Category: Dehydration of polyketide intermediate]]
		+	[[Category: Double hotdog fold]]
		+	[[Category: Lyase]]
		+	[[Category: Module 10 of rifamycin polyketide synthase]]

OCA at 07:30, 29 September 2013

OCA — Sun, 29 Sep 2013 07:30:18 GMT

←Older revision		Revision as of 07:30, 29 September 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ln9 is ON HOLD	+	The entry 4ln9 is ON HOLD until Paper Publication

	Authors: Gay, D.C., You, Y.-O., Cane, D., Keatinge-Clay, A.T.		Authors: Gay, D.C., You, Y.-O., Cane, D., Keatinge-Clay, A.T.

	Description: Crystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase		Description: Crystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase

OCA: Protected "4ln9" [edit=sysop:move=sysop]

OCA — Thu, 18 Jul 2013 04:48:46 GMT

Protected "4ln9" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:48, 18 July 2013

OCA: New page: '''Unreleased structure''' The entry 4ln9 is ON HOLD Authors: Gay, D.C., You, Y.-O., Cane, D., Keatinge-Clay, A.T. Description: Crystal structure of the dehydratase domain from the ter...

OCA — Thu, 18 Jul 2013 04:48:46 GMT

New page: '''Unreleased structure''' The entry 4ln9 is ON HOLD Authors: Gay, D.C., You, Y.-O., Cane, D., Keatinge-Clay, A.T. Description: Crystal structure of the dehydratase domain from the ter...

New page

'''Unreleased structure'''

The entry 4ln9 is ON HOLD

Authors: Gay, D.C., You, Y.-O., Cane, D., Keatinge-Clay, A.T.

Description: Crystal structure of the dehydratase domain from the terminal module of the rifamycin polyketide synthase