This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.




1hb3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:23, 13 December 2023) (edit) (undo)
 
(19 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1hb3.jpg|left|200px]]<br /><applet load="1hb3" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1hb3, resolution 1.40&Aring;" />
 
-
'''ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED PRODUCT FROM ANAEROBIC ACOV FE COMPLEX)'''<br />
 
-
==Overview==
+
==ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED PRODUCT FROM ANAEROBIC ACOV FE COMPLEX)==
-
BACKGROUND: Isopenicillin N synthase (IPNS) catalyses formation of, bicyclic isopenicillin N, precursor to all penicillin and cephalosporin, antibiotics, from the linear tripeptide, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine. IPNS is a non-haem, iron(II)-dependent enzyme which utilises the full oxidising potential of, molecular oxygen in catalysing the bicyclisation reaction. The reaction, mechanism is believed to involve initial formation of the beta-lactam ring, (via a thioaldehyde intermediate) to give an iron(IV)-oxo species, which, then mediates closure of the 5-membered thiazolidine ring. RESULTS: Here, we report experiments employing time-resolved crystallography to observe, turnover of an isosteric substrate analogue designed to intercept the, catalytic pathway at an early stage. Reaction in the crystalline, enzyme-substrate complex was initiated by the application of high-pressure, oxygen, and subsequent flash freezing allowed an oxygenated product to be, trapped, bound at the iron centre. A mechanism for formation of the, observed thiocarboxylate product is proposed. CONCLUSIONS: In the absence, of its natural reaction partner (the N-H proton of the, L-cysteinyl-D-valine amide bond), the proposed hydroperoxide intermediate, appears to attack the putative thioaldehyde species directly. These, results shed light on the events preceding beta-lactam closure in the IPNS, reaction cycle, and enhance our understanding of the mechanism for, reaction of the enzyme with its natural substrate.
+
<StructureSection load='1hb3' size='340' side='right'caption='[[1hb3]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1hb3]] 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=1HB3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HB3 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]] 1.4&#8491;</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=SCV:N6-[(1S)-2-{[(1R)-1-CARBOXY-2-METHYLPROPYL]OXY}-1-(MERCAPTOCARBONYL)-2-OXOETHYL]-6-OXO-L-LYSINE'>SCV</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=1hb3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hb3 OCA], [https://pdbe.org/1hb3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hb3 RCSB], [https://www.ebi.ac.uk/pdbsum/1hb3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hb3 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/hb/1hb3_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=1hb3 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
BACKGROUND: Isopenicillin N synthase (IPNS) catalyses formation of bicyclic isopenicillin N, precursor to all penicillin and cephalosporin antibiotics, from the linear tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine. IPNS is a non-haem iron(II)-dependent enzyme which utilises the full oxidising potential of molecular oxygen in catalysing the bicyclisation reaction. The reaction mechanism is believed to involve initial formation of the beta-lactam ring (via a thioaldehyde intermediate) to give an iron(IV)-oxo species, which then mediates closure of the 5-membered thiazolidine ring. RESULTS: Here we report experiments employing time-resolved crystallography to observe turnover of an isosteric substrate analogue designed to intercept the catalytic pathway at an early stage. Reaction in the crystalline enzyme-substrate complex was initiated by the application of high-pressure oxygen, and subsequent flash freezing allowed an oxygenated product to be trapped, bound at the iron centre. A mechanism for formation of the observed thiocarboxylate product is proposed. CONCLUSIONS: In the absence of its natural reaction partner (the N-H proton of the L-cysteinyl-D-valine amide bond), the proposed hydroperoxide intermediate appears to attack the putative thioaldehyde species directly. These results shed light on the events preceding beta-lactam closure in the IPNS reaction cycle, and enhance our understanding of the mechanism for reaction of the enzyme with its natural substrate.
-
==About this Structure==
+
Alternative oxidation by isopenicillin N synthase observed by X-ray diffraction.,Ogle JM, Clifton IJ, Rutledge PJ, Elkins JM, Burzlaff NI, Adlington RM, Roach PL, Baldwin JE Chem Biol. 2001 Dec;8(12):1231-7. PMID:11755401<ref>PMID:11755401</ref>
-
1HB3 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Emericella_nidulans Emericella nidulans] with SO4, FE2 and SCV as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Site: <scene name='pdbsite=SCV:Active Site (Fe Binding)'>SCV</scene>. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1HB3 OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Alternative oxidation by isopenicillin N synthase observed by X-ray diffraction., Ogle JM, Clifton IJ, Rutledge PJ, Elkins JM, Burzlaff NI, Adlington RM, Roach PL, Baldwin JE, Chem Biol. 2001 Dec;8(12):1231-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11755401 11755401]
+
</div>
-
[[Category: Emericella nidulans]]
+
<div class="pdbe-citations 1hb3" style="background-color:#fffaf0;"></div>
-
[[Category: Single protein]]
+
-
[[Category: Adlington, R.M.]]
+
-
[[Category: Baldwin, J.E.]]
+
-
[[Category: Burzlaff, N.I.]]
+
-
[[Category: Clifton, I.J.]]
+
-
[[Category: Elkins, J.M.]]
+
-
[[Category: Ogle, J.M.]]
+
-
[[Category: Roach, P.L.]]
+
-
[[Category: Rutledge, P.J.]]
+
-
[[Category: FE2]]
+
-
[[Category: SCV]]
+
-
[[Category: SO4]]
+
-
[[Category: antibiotic biosynthesis]]
+
-
[[Category: b-lactam antibiotic]]
+
-
[[Category: oxygenase]]
+
-
[[Category: penicillin biosynthesis]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Dec 18 16:13:22 2007''
+
==See Also==
 +
*[[Isopenicillin N synthase|Isopenicillin N synthase]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Aspergillus nidulans]]
 +
[[Category: Large Structures]]
 +
[[Category: Adlington RM]]
 +
[[Category: Baldwin JE]]
 +
[[Category: Burzlaff NI]]
 +
[[Category: Clifton IJ]]
 +
[[Category: Elkins JM]]
 +
[[Category: Ogle JM]]
 +
[[Category: Roach PL]]
 +
[[Category: Rutledge PJ]]

Current revision

ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN EXPOSED PRODUCT FROM ANAEROBIC ACOV FE COMPLEX)

PDB ID 1hb3

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1hb3"
Personal tools