1oc1: Difference between revisions

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-[[Image:1oc1.png|left|200px]]
-<!--
+==ISOPENICILLIN N SYNTHASE aminoadipoyl-cysteinyl-aminobutyrate-FE COMPLEX==
-The line below this paragraph, containing "STRUCTURE_1oc1", creates the "Structure Box" on the page.
+<StructureSection load='1oc1' size='340' side='right'caption='[[1oc1]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1oc1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_nidulans Aspergillus nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OC1 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASV:DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-D-VINYLGLYCINE'>ASV</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_1oc1|  PDB=1oc1  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oc1 OCA], [https://pdbe.org/1oc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oc1 RCSB], [https://www.ebi.ac.uk/pdbsum/1oc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oc1 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>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oc/1oc1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1oc1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Isopenicillin N synthase (IPNS) is a non-haem iron(II) oxidase which catalyses the biosynthesis of isopenicillin N from the tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV). Herein we report crystallographic studies to investigate the reaction of IPNS with the truncated substrate analogue delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-alpha-aminobutyrate (ACAb). It has been reported previously that this analogue gives rise to three beta-lactam products when incubated with IPNS: two methyl penams and a cepham. Crystal structures of the IPNS-Fe(II)-ACAb and IPNS-Fe(II)-ACAb-NO complexes have now been solved and are reported herein. These structures and modelling studies based on them shed light on the diminished product selectivity shown by IPNS in its reaction with ACAb and further rationalize the presence of certain key residues at the IPNS active site.
-===ISOPENICILLIN N SYNTHASE AMINOADIPOYL-CYSTEINYL-AMINOBUTYRATE-FE COMPLEX===
+Structural studies on the reaction of isopenicillin N synthase with the substrate analogue delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-alpha-aminobutyrate.,Long AJ, Clifton IJ, Roach PL, Baldwin JE, Schofield CJ, Rutledge PJ Biochem J. 2003 Jun 15;372(Pt 3):687-93. PMID:12622704<ref>PMID:12622704</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1oc1" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12622704}}, adds the Publication Abstract to the page
+*[[Isopenicillin N synthase|Isopenicillin N synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12622704 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12622704}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Aspergillus nidulans]]
-[[1oc1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OC1 OCA].
+[[Category: Large Structures]]
+[[Category: Baldwin JE]]
-==Reference==
+[[Category: Clifton IJ]]
-<ref group="xtra">PMID:12622704</ref><ref group="xtra">PMID:9194566</ref><references group="xtra"/>
+[[Category: Long AJ]]
-[[Category: Emericella nidulans]]
+[[Category: Roach PL]]
-[[Category: Baldwin, J E.]]
+[[Category: Rutledge PJ]]
-[[Category: Clifton, I J.]]
+[[Category: Schofield CJ]]
-[[Category: Long, A J.]]
-[[Category: Roach, P L.]]
-[[Category: Rutledge, P J.]]
-[[Category: Schofield, C J.]]
-[[Category: B-lactam antibiotic]]
-[[Category: Oxidoreductase]]
-[[Category: Oxygenase]]
-[[Category: Penicillin biosynthesis]]