6y0o - Revision history

OCA at 13:16, 24 January 2024

OCA — Wed, 24 Jan 2024 13:16:39 GMT

←Older revision		Revision as of 13:16, 24 January 2024
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	<StructureSection load='6y0o' size='340' side='right'caption='[[6y0o]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6y0o' size='340' side='right'caption='[[6y0o]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y0o]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aspergillus_nidulans~~ Aspergillus nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y0O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6Y0O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y0o]] 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=6Y0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y0O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACV:L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE'>ACV</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bk0\|1bk0]], [[1blz\|1blz]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACV:L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE'>ACV</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ipnA (ips) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227321 Aspergillus nidulans])</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=6y0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0o OCA], [https://pdbe.org/6y0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y0o RCSB], [https://www.ebi.ac.uk/pdbsum/6y0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0o 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/Isopenicillin-N_synthase Isopenicillin-N synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.21.3.1 1.21.3.1] </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=6y0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0o OCA], [~~http~~://pdbe.org/6y0o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6y0o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6y0o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0o ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~IPNS_EMENI IPNS_EMENI~~]~~] Removes, in~~ the ~~presence~~ of ~~oxygen~~, ~~4 hydrogen atoms from delta~~-L-(~~alpha~~-~~aminoadipyl~~)-L-cysteinyl-D-valine (ACV) to ~~form~~ the ~~azetidinone and thiazolidine rings of~~ isopenicillin.	+	[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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6y0o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6y0o" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Isopenicillin N synthase\|Isopenicillin N synthase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Aspergillus nidulans]]	+	[[Category: Aspergillus nidulans FGSC A4]]
-	~~[[Category: Isopenicillin-N synthase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aller, P]]	+	[[Category: Aller P]]
-	[[Category: Axford, D]]	+	[[Category: Axford D]]
-	[[Category: Beale~~, J H~~]]	+	[[Category: Beale JH]]
-	[[Category: Butryn, A]]	+	[[Category: Butryn A]]
-	[[Category: Dirr~~, A S~~]]	+	[[Category: Dirr AS]]
-	[[Category: Kamps~~, J J.A G~~]]	+	[[Category: Kamps JJAG]]
-	[[Category: Lang~~, P A~~]]	+	[[Category: Lang PA]]
-	[[Category: Leissing~~, T M~~]]	+	[[Category: Leissing TM]]
-	[[Category: McDonough~~, M A~~]]	+	[[Category: McDonough MA]]
-	[[Category: Orville~~, A M~~]]	+	[[Category: Orville AM]]
-	[[Category: Owen, R]]	+	[[Category: Owen R]]
-	[[Category: Rabe, P]]	+	[[Category: Rabe P]]
-	[[Category: Schofield~~, C J]]~~	+	[[Category: Schofield CJ]]
-	~~[[Category: Iron dependent oxygenase]]~~	+
-	~~[[Category: Isopenicillin n]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Penicillin biosynthesis~~]]	+

OCA at 07:46, 30 September 2020

OCA — Wed, 30 Sep 2020 07:46:05 GMT

←Older revision		Revision as of 07:46, 30 September 2020
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	==isopenicillin N synthase in complex with ACV and Fe under anaerobic environment using FT-SSX methods==		==isopenicillin N synthase in complex with ACV and Fe under anaerobic environment using FT-SSX methods==
-	<StructureSection load='6y0o' size='340' side='right'caption='[[6y0o]]' scene=''>	+	<StructureSection load='6y0o' size='340' side='right'caption='[[6y0o]], [[Resolution\|resolution]] 2.20Å' 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=6Y0O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y0O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y0o]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspergillus_nidulans Aspergillus nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y0O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y0O FirstGlance]. <br>
-	</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=6y0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0o OCA], [http://pdbe.org/6y0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y0o RCSB], [http://www.ebi.ac.uk/pdbsum/6y0o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0o ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACV:L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE'>ACV</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1bk0\|1bk0]], [[1blz\|1blz]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ipnA (ips) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=227321 Aspergillus nidulans])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isopenicillin-N_synthase Isopenicillin-N synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.21.3.1 1.21.3.1] </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=6y0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0o OCA], [http://pdbe.org/6y0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y0o RCSB], [http://www.ebi.ac.uk/pdbsum/6y0o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0o ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/IPNS_EMENI IPNS_EMENI]] Removes, in the presence of oxygen, 4 hydrogen atoms from delta-L-(alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV) to form the azetidinone and thiazolidine rings of isopenicillin.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cryogenic X-ray diffraction is a powerful tool for crystallographic studies on enzymes including oxygenases and oxidases. Amongst the benefits that cryo-conditions (usually employing a nitro-gen cryo-stream at 100 K) enable, is data collection of di-oxy-gen-sensitive samples. Although not strictly anaerobic, at low temperatures the vitreous ice conditions severely restrict O2 diffusion into and/or through the protein crystal. Cryo-conditions limit chemical reactivity, including reactions that require significant conformational changes. By contrast, data collection at room temperature imposes fewer restrictions on diffusion and reactivity; room-temperature serial methods are thus becoming common at synchrotrons and XFELs. However, maintaining an anaerobic environment for di-oxy-gen-dependent enzymes has not been explored for serial room-temperature data collection at synchrotron light sources. This work describes a methodology that employs an adaptation of the 'sheet-on-sheet' sample mount, which is suitable for the low-dose room-temperature data collection of anaerobic samples at synchrotron light sources. The method is characterized by easy sample preparation in an anaerobic glovebox, gentle handling of crystals, low sample consumption and preservation of a localized anaerobic environment over the timescale of the experiment (<5 min). The utility of the method is highlighted by studies with three X-ray-radiation-sensitive Fe(II)-containing model enzymes: the 2-oxoglutarate-dependent l-arginine hy-droxy-lase VioC and the DNA repair enzyme AlkB, as well as the oxidase isopenicillin N synthase (IPNS), which is involved in the biosynthesis of all penicillin and cephalosporin antibiotics.
		+
		+	Anaerobic fixed-target serial crystallography.,Rabe P, Beale JH, Butryn A, Aller P, Dirr A, Lang PA, Axford DN, Carr SB, Leissing TM, McDonough MA, Davy B, Ebrahim A, Orlans J, Storm SLS, Orville AM, Schofield CJ, Owen RL IUCrJ. 2020 Aug 21;7(Pt 5):901-912. doi: 10.1107/S2052252520010374. eCollection, 2020 Sep 1. PMID:32939282<ref>PMID:32939282</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y0o" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspergillus nidulans]]
		+	[[Category: Isopenicillin-N synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aller P]]	+	[[Category: Aller, P]]
-	[[Category: Axford D]]	+	[[Category: Axford, D]]
-	[[Category: Beale JH]]	+	[[Category: Beale, J H]]
-	[[Category: Butryn A]]	+	[[Category: Butryn, A]]
-	[[Category: Dirr AS]]	+	[[Category: Dirr, A S]]
-	[[Category: Kamps ~~JJAG~~]]	+	[[Category: Kamps, J J.A G]]
-	[[Category: Lang PA]]	+	[[Category: Lang, P A]]
-	[[Category: Leissing TM]]	+	[[Category: Leissing, T M]]
-	[[Category: McDonough MA]]	+	[[Category: McDonough, M A]]
-	[[Category: Orville AM]]	+	[[Category: Orville, A M]]
-	[[Category: Owen R]]	+	[[Category: Owen, R]]
-	[[Category: Rabe P]]	+	[[Category: Rabe, P]]
-	[[Category: Schofield CJ]]	+	[[Category: Schofield, C J]]
		+	[[Category: Iron dependent oxygenase]]
		+	[[Category: Isopenicillin n]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Penicillin biosynthesis]]

OCA at 09:34, 9 September 2020

OCA — Wed, 09 Sep 2020 09:34:53 GMT

←Older revision		Revision as of 09:34, 9 September 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6y0o is ~~ON HOLD until Paper Publication~~	+	==isopenicillin N synthase in complex with ACV and Fe under anaerobic environment using FT-SSX methods==
-		+	<StructureSection load='6y0o' size='340' side='right'caption='[[6y0o]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y0O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6Y0O FirstGlance]. <br>
-	~~Description~~:	+	</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=6y0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y0o OCA], [http://pdbe.org/6y0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6y0o RCSB], [http://www.ebi.ac.uk/pdbsum/6y0o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6y0o ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Aller P]]
		+	[[Category: Axford D]]
		+	[[Category: Beale JH]]
		+	[[Category: Butryn A]]
		+	[[Category: Dirr AS]]
		+	[[Category: Kamps JJAG]]
		+	[[Category: Lang PA]]
		+	[[Category: Leissing TM]]
		+	[[Category: McDonough MA]]
		+	[[Category: Orville AM]]
		+	[[Category: Owen R]]
		+	[[Category: Rabe P]]
		+	[[Category: Schofield CJ]]

OCA at 04:21, 22 April 2020

OCA — Wed, 22 Apr 2020 04:21:21 GMT

←Older revision		Revision as of 04:21, 22 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y0o is ON HOLD	+	The entry 6y0o is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6y0o" [edit=sysop:move=sysop]

OCA — Wed, 19 Feb 2020 05:25:37 GMT

Protected "6y0o" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:25, 19 February 2020

OCA: New page: '''Unreleased structure''' The entry 6y0o is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Feb 2020 05:25:36 GMT

New page: '''Unreleased structure''' The entry 6y0o is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6y0o is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]