6zaq - Revision history

OCA at 13:45, 24 January 2024

OCA — Wed, 24 Jan 2024 13:45:29 GMT

←Older revision		Revision as of 13:45, 24 January 2024
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	==Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and IPN after dioxygen exposure==		==Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and IPN after dioxygen exposure==
-	<StructureSection load='6zaq' size='340' side='right'caption='[[6zaq]]' scene=''>	+	<StructureSection load='6zaq' size='340' side='right'caption='[[6zaq]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZAQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6zaq]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_nidulans_FGSC_A4 Aspergillus nidulans FGSC A4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZAQ 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=6zaq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zaq OCA], [https://pdbe.org/6zaq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zaq RCSB], [https://www.ebi.ac.uk/pdbsum/6zaq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zaq 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]] 1.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=IP1:ISOPENICILLIN+N'>IP1</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6zaq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zaq OCA], [https://pdbe.org/6zaq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zaq RCSB], [https://www.ebi.ac.uk/pdbsum/6zaq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zaq ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/IPNA_EMENI IPNA_EMENI] Isopenicillin N synthase; part of the gene cluster that mediates the biosynthesis of penicillin, the world's most important antibiotic (PubMed:3319778, PubMed:11755401). IpnA catalyzes the cyclization of the tripeptide N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine (LLD-ACV or ACV) to form isopenicillin N (IPN) that contains the beta-lactam nucleus (PubMed:3319778, PubMed:11755401, PubMed:28703303). The penicillin biosynthesis occurs via 3 enzymatic steps, the first corresponding to the production of the tripeptide N-[(5S)-5-amino-5-carboxypentanoyl]-L-cysteinyl-D-valine (LLD-ACV or ACV) by the NRPS acvA. The tripeptide ACV is then cyclized to isopenicillin N (IPN) by the isopenicillin N synthase ipnA that forms the beta-lactam nucleus. Finally, the alpha-aminoadipyl side chain is exchanged for phenylacetic acid by the isopenicillin N acyltransferase penDE to yield penicillin in the peroxisomal matrix (By similarity).[UniProtKB:P08703]<ref>PMID:11755401</ref> <ref>PMID:28703303</ref> <ref>PMID:3319778</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Isopenicillin N synthase (IPNS) catalyzes the unique reaction of l-delta-(alpha-aminoadipoyl)-l-cysteinyl-d-valine (ACV) with dioxygen giving isopenicillin N (IPN), the precursor of all natural penicillins and cephalosporins. X-ray free-electron laser studies including time-resolved crystallography and emission spectroscopy reveal how reaction of IPNS:Fe(II):ACV with dioxygen to yield an Fe(III) superoxide causes differences in active site volume and unexpected conformational changes that propagate to structurally remote regions. Combined with solution studies, the results reveal the importance of protein dynamics in regulating intermediate conformations during conversion of ACV to IPN. The results have implications for catalysis by multiple IPNS-related oxygenases, including those involved in the human hypoxic response, and highlight the power of serial femtosecond crystallography to provide insight into long-range enzyme dynamics during reactions presently impossible for nonprotein catalysts.
		+
		+	X-ray free-electron laser studies reveal correlated motion during isopenicillin N synthase catalysis.,Rabe P, Kamps JJAG, Sutherlin KD, Linyard JDS, Aller P, Pham CC, Makita H, Clifton I, McDonough MA, Leissing TM, Shutin D, Lang PA, Butryn A, Brem J, Gul S, Fuller FD, Kim IS, Cheah MH, Fransson T, Bhowmick A, Young ID, O'Riordan L, Brewster AS, Pettinati I, Doyle M, Joti Y, Owada S, Tono K, Batyuk A, Hunter MS, Alonso-Mori R, Bergmann U, Owen RL, Sauter NK, Claridge TDW, Robinson CV, Yachandra VK, Yano J, Kern JF, Orville AM, Schofield CJ Sci Adv. 2021 Aug 20;7(34):eabh0250. doi: 10.1126/sciadv.abh0250. Print 2021 Aug. PMID:34417180<ref>PMID:34417180</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zaq" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Isopenicillin N synthase\|Isopenicillin N synthase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspergillus nidulans FGSC A4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Aller P]]		[[Category: Aller P]]

OCA at 12:11, 9 June 2021

OCA — Wed, 09 Jun 2021 12:11:08 GMT

←Older revision		Revision as of 12:11, 9 June 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6zaq ~~is ON HOLD until Paper Publication~~	+	==Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and IPN after dioxygen exposure==
-		+	<StructureSection load='6zaq' size='340' side='right'caption='[[6zaq]]' scene=''>
-	~~Authors~~: ~~Rabe, P~~.~~, Kamps, J~~.J.A.G.~~, Sutherlin, K~~.~~, Pharm, C~~.~~, McDonough, M~~.A., ~~Leissing, T~~.M.~~, Aller, P~~., ~~Butryn, A~~., ~~Linyard, J~~.~~, Lang, P~~.~~, Brem, J~~., ~~Fuller, F~~.D.~~, Batyuk, A~~., ~~Hunter, M~~.~~S., Pettinati, I., Clifton, I.J., Alonso~~-~~Mori, R., Gul, S., Young, I., Kim, I., Bhowmick, A., ORiordan, L., Brewster, A.S., Claridge, T.D.W., Sauter, N.K., Yachandra, V., Yano, J., Kern, J.F., Orville, A.M., Schofield, C.J~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZAQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZAQ FirstGlance]. <br>
-	~~Description: Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and IPN after dioxygen exposure~~	+	</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=6zaq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zaq OCA], [https://pdbe.org/6zaq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zaq RCSB], [https://www.ebi.ac.uk/pdbsum/6zaq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zaq ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Yachandra, V~~]]	+	__TOC__
-	[[Category: ~~Claridge, T.D.W~~]]	+	</StructureSection>
-	[[Category: ~~Clifton, I.J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Oriordan, L~~]]	+	[[Category: Aller P]]
-	[[Category: ~~Linyard,~~ J]]	+	[[Category: Alonso-Mori R]]
-	[[Category: ~~Hunter, M.S~~]]	+	[[Category: Batyuk A]]
-	[[Category: ~~Brem, J~~]]	+	[[Category: Bhowmick A]]
-	[[Category: ~~Orville, A.M~~]]	+	[[Category: Brem J]]
-	[[Category: ~~Fuller, F.D~~]]	+	[[Category: Brewster AS]]
-	[[Category: ~~Kern, J.F~~]]	+	[[Category: Butryn A]]
-	[[Category: ~~Sauter, N.K~~]]	+	[[Category: Claridge TDW]]
-	[[Category: ~~Kim, I~~]]	+	[[Category: Clifton IJ]]
-	[[Category: ~~Young, I~~]]	+	[[Category: Fuller FD]]
-	[[Category: ~~Pharm, C~~]]	+	[[Category: Gul S]]
-	[[Category: ~~Brewster, A.S~~]]	+	[[Category: Hunter MS]]
-	[[Category: ~~Yano, J~~]]	+	[[Category: Kamps JJAG]]
-	[[Category: ~~Aller, P~~]]	+	[[Category: Kern JF]]
-	[[Category: ~~Rabe, P~~]]	+	[[Category: Kim I]]
-	[[Category: ~~Pettinati, I~~]]	+	[[Category: Lang P]]
-	[[Category: ~~Mcdonough, M.A~~]]	+	[[Category: Leissing TM]]
-	[[Category: ~~Sutherlin, K~~]]	+	[[Category: Linyard J]]
-	[[Category: ~~Lang, P~~]]	+	[[Category: McDonough MA]]
-	[[Category: ~~Kamps, J.J.A.G~~]]	+	[[Category: ORiordan L]]
-	[[Category: ~~Leissing, T.M~~]]	+	[[Category: Orville AM]]
-	[[Category: ~~Batyuk, A~~]]	+	[[Category: Pettinati I]]
-	[[Category: ~~Bhowmick, A~~]]	+	[[Category: Pharm C]]
-	[[Category: ~~Gul, S~~]]	+	[[Category: Rabe P]]
-	[[Category: ~~Butryn, A~~]]	+	[[Category: Sauter NK]]
-	[[Category: ~~Schofield, C.~~J]]	+	[[Category: Schofield CJ]]
-	[[Category: ~~Alonso-Mori, R~~]]	+	[[Category: Sutherlin K]]
		+	[[Category: Yachandra V]]
		+	[[Category: Yano J]]
		+	[[Category: Young I]]

OCA at 11:03, 8 July 2020

OCA — Wed, 08 Jul 2020 11:03:59 GMT

←Older revision		Revision as of 11:03, 8 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6zaq is ON HOLD	+	The entry 6zaq is ON HOLD until Paper Publication

	Authors: Rabe, P., Kamps, J.J.A.G., Sutherlin, K., Pharm, C., McDonough, M.A., Leissing, T.M., Aller, P., Butryn, A., Linyard, J., Lang, P., Brem, J., Fuller, F.D., Batyuk, A., Hunter, M.S., Pettinati, I., Clifton, I.J., Alonso-Mori, R., Gul, S., Young, I., Kim, I., Bhowmick, A., ORiordan, L., Brewster, A.S., Claridge, T.D.W., Sauter, N.K., Yachandra, V., Yano, J., Kern, J.F., Orville, A.M., Schofield, C.J.		Authors: Rabe, P., Kamps, J.J.A.G., Sutherlin, K., Pharm, C., McDonough, M.A., Leissing, T.M., Aller, P., Butryn, A., Linyard, J., Lang, P., Brem, J., Fuller, F.D., Batyuk, A., Hunter, M.S., Pettinati, I., Clifton, I.J., Alonso-Mori, R., Gul, S., Young, I., Kim, I., Bhowmick, A., ORiordan, L., Brewster, A.S., Claridge, T.D.W., Sauter, N.K., Yachandra, V., Yano, J., Kern, J.F., Orville, A.M., Schofield, C.J.

OCA: Protected "6zaq" [edit=sysop:move=sysop]

OCA — Wed, 17 Jun 2020 08:51:50 GMT

Protected "6zaq" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:51, 17 June 2020

OCA: New page: '''Unreleased structure''' The entry 6zaq is ON HOLD Authors: Rabe, P., Kamps, J.J.A.G., Sutherlin, K., Pharm, C., McDonough, M.A., Leissing, T.M., Aller, P., Butryn, A., Linyard, J., L...

OCA — Wed, 17 Jun 2020 08:51:49 GMT

New page: '''Unreleased structure''' The entry 6zaq is ON HOLD Authors: Rabe, P., Kamps, J.J.A.G., Sutherlin, K., Pharm, C., McDonough, M.A., Leissing, T.M., Aller, P., Butryn, A., Linyard, J., L...

New page

'''Unreleased structure'''

The entry 6zaq is ON HOLD

Authors: Rabe, P., Kamps, J.J.A.G., Sutherlin, K., Pharm, C., McDonough, M.A., Leissing, T.M., Aller, P., Butryn, A., Linyard, J., Lang, P., Brem, J., Fuller, F.D., Batyuk, A., Hunter, M.S., Pettinati, I., Clifton, I.J., Alonso-Mori, R., Gul, S., Young, I., Kim, I., Bhowmick, A., ORiordan, L., Brewster, A.S., Claridge, T.D.W., Sauter, N.K., Yachandra, V., Yano, J., Kern, J.F., Orville, A.M., Schofield, C.J.

Description: Room temperature XFEL Isopenicillin N synthase structure in complex with Fe and IPN after dioxygen exposure
[[Category: Unreleased Structures]]
[[Category: Yachandra, V]]
[[Category: Claridge, T.D.W]]
[[Category: Clifton, I.J]]
[[Category: Oriordan, L]]
[[Category: Linyard, J]]
[[Category: Hunter, M.S]]
[[Category: Brem, J]]
[[Category: Orville, A.M]]
[[Category: Fuller, F.D]]
[[Category: Kern, J.F]]
[[Category: Sauter, N.K]]
[[Category: Kim, I]]
[[Category: Young, I]]
[[Category: Pharm, C]]
[[Category: Brewster, A.S]]
[[Category: Yano, J]]
[[Category: Aller, P]]
[[Category: Rabe, P]]
[[Category: Pettinati, I]]
[[Category: Mcdonough, M.A]]
[[Category: Sutherlin, K]]
[[Category: Lang, P]]
[[Category: Kamps, J.J.A.G]]
[[Category: Leissing, T.M]]
[[Category: Batyuk, A]]
[[Category: Bhowmick, A]]
[[Category: Gul, S]]
[[Category: Butryn, A]]
[[Category: Schofield, C.J]]
[[Category: Alonso-Mori, R]]