7psw: Difference between revisions
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The | ==Spin labeled IPNS S55C variant in complex with Fe and ACV under anaerobic conditions== | ||
<StructureSection load='7psw' size='340' side='right'caption='[[7psw]], [[Resolution|resolution]] 1.21Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[7psw]] 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=7PSW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PSW FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.21Å</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=GOL:GLYCEROL'>GOL</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=7psw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7psw OCA], [https://pdbe.org/7psw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7psw RCSB], [https://www.ebi.ac.uk/pdbsum/7psw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7psw ProSAT]</span></td></tr> | |||
</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) catalyses formation of the beta-lactam and thiazolidine rings of isopenicillin N (IPN) from its linear tripeptide L-delta-(alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV) substrate in an iron and dioxygen (O2) dependent four electron oxidation without precedent in current synthetic chemistry. Recent X-ray free electron laser (XFEL) studies including time-resolved serial femtosecond crystallography show binding of O2 to the IPNS:Fe(II):ACV complex induces unexpected conformational changes in alpha-helices on the surface of IPNS, in particular in alpha3 and alpha10. However, how substrate binding leads to conformational changes away from the active site is unknown. Here, using detailed (19)F NMR and EPR experiments with labelled IPNS variants, we investigated motions in alpha3 and alpha10 induced by binding of ferrous iron, ACV and the O2 analogue NO, using the less mobile alpha6 for comparison. (19)F NMR studies were carried out on singly and doubly labelled alpha3, alpha6 and alpha10 variants at different temperatures. In addition, double electron-electron resonance (DEER) EPR analysis was carried out on doubly spin labelled variants. The combined spectroscopic and crystallographic results reveal that substantial conformational changes in regions of IPNS including alpha3 and alpha10 are induced by binding of ACV and NO. Since IPNS is a member of the structural superfamily of 2-oxoglutarate dependent oxygenases and related enzymes, related conformational changes may be of general importance in non-heme oxygenase catalysis. | |||
Spectroscopic studies reveal details of substrate-induced conformational changes distant from the active site in isopenicillin N synthase.,Rabe P, Walla CC, Goodyear NK, Welsh J, Southwart R, Clifton I, Linyard JDS, Tumber A, Claridge TDW, Myers WK, Schofield CJ J Biol Chem. 2022 Jul 11:102249. doi: 10.1016/j.jbc.2022.102249. PMID:35835215<ref>PMID:35835215</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7psw" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Isopenicillin N synthase|Isopenicillin N synthase]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Aspergillus nidulans FGSC A4]] | |||
[[Category: Large Structures]] | |||
[[Category: Clifton I]] | |||
[[Category: Rabe P]] | |||
[[Category: Schofield CJ]] | |||
[[Category: Walla C]] | |||
Latest revision as of 16:08, 1 February 2024
Spin labeled IPNS S55C variant in complex with Fe and ACV under anaerobic conditionsSpin labeled IPNS S55C variant in complex with Fe and ACV under anaerobic conditions
Structural highlights
FunctionIPNA_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][1] [2] [3] Publication Abstract from PubMedIsopenicillin N synthase (IPNS) catalyses formation of the beta-lactam and thiazolidine rings of isopenicillin N (IPN) from its linear tripeptide L-delta-(alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV) substrate in an iron and dioxygen (O2) dependent four electron oxidation without precedent in current synthetic chemistry. Recent X-ray free electron laser (XFEL) studies including time-resolved serial femtosecond crystallography show binding of O2 to the IPNS:Fe(II):ACV complex induces unexpected conformational changes in alpha-helices on the surface of IPNS, in particular in alpha3 and alpha10. However, how substrate binding leads to conformational changes away from the active site is unknown. Here, using detailed (19)F NMR and EPR experiments with labelled IPNS variants, we investigated motions in alpha3 and alpha10 induced by binding of ferrous iron, ACV and the O2 analogue NO, using the less mobile alpha6 for comparison. (19)F NMR studies were carried out on singly and doubly labelled alpha3, alpha6 and alpha10 variants at different temperatures. In addition, double electron-electron resonance (DEER) EPR analysis was carried out on doubly spin labelled variants. The combined spectroscopic and crystallographic results reveal that substantial conformational changes in regions of IPNS including alpha3 and alpha10 are induced by binding of ACV and NO. Since IPNS is a member of the structural superfamily of 2-oxoglutarate dependent oxygenases and related enzymes, related conformational changes may be of general importance in non-heme oxygenase catalysis. Spectroscopic studies reveal details of substrate-induced conformational changes distant from the active site in isopenicillin N synthase.,Rabe P, Walla CC, Goodyear NK, Welsh J, Southwart R, Clifton I, Linyard JDS, Tumber A, Claridge TDW, Myers WK, Schofield CJ J Biol Chem. 2022 Jul 11:102249. doi: 10.1016/j.jbc.2022.102249. PMID:35835215[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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