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2x1d

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Current revision

The crystal structure of mature acyl coenzyme A:isopenicillin N acyltransferase from Penicillium chrysogenum

Structural highlights

2x1d is a 4 chain structure with sequence from Penicillium chrysogenum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.64Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

AATA_PENCH Isopenicillin-N N-acyltransferase; part of the gene cluster that mediates the biosynthesis of penicillin, the world's most important antibiotic (PubMed:1368505, PubMed:2110531, PubMed:2120195). AatA catalyzes the exchange of the alpha-aminoadipyl side chain of isopenicillin N for phenylacetic acid to yield penicillin (PubMed:1368505, PubMed:2110531, PubMed:2120195). This step occurs in the peroxisomal matrix and the penM and paaT transporters are involved in the isopenicillin N and phenylacetic acid import into the peroxisome, respectively (PubMed:23053082). 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 aatA to yield penicillin in the peroxisomal matrix (Probable) (PubMed:1368505).^[1] ^[2] ^[3] ^[4] ^[5]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Penicillium chrysogenum Acyl coenzyme A:isopenicillin N acyltransferase (AT) performs the last step in the biosynthesis of hydrophobic penicillins, exchanging the hydrophilic side chain of a precursor for various hydrophobic side chains. Like other N-terminal nucleophile hydrolases AT is produced as an inactive precursor that matures upon posttranslational cleavage. The structure of a Cys103Ala precursor mutant shows that maturation is autoproteolytic, initiated by Cys103 cleaving its preceding peptide bond. The crystal structure of the mature enzyme shows that after autoproteolysis residues 92-102 fold outwards, exposing a buried pocket. This pocket is structurally and chemically flexible and can accommodate substrates of different size and polarity. Modeling of a substrate-bound state indicates the residues important for catalysis. Comparison of the proposed autoproteolytic and substrate hydrolysis mechanisms shows that in both events the same catalytic residues are used, but that they perform different roles in catalysis.

Structures of an isopenicillin N converting Ntn-hydrolase reveal different catalytic roles for the active site residues of precursor and mature enzyme.,Bokhove M, Yoshida H, Hensgens CM, van der Laan JM, Sutherland JD, Dijkstra BW Structure. 2010 Mar 10;18(3):301-8. PMID:20223213^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Smith DJ, Burnham MK, Edwards J, Earl AJ, Turner G. Cloning and heterologous expression of the penicillin biosynthetic gene cluster from penicillum chrysogenum. Biotechnology (N Y). 1990 Jan;8(1):39-41. PMID:1368505 doi:10.1038/nbt0190-39
↑ Whiteman PA, Abraham EP, Baldwin JE, Fleming MD, Schofield CJ, Sutherland JD, Willis AC. Acyl coenzyme A: 6-aminopenicillanic acid acyltransferase from Penicillium chrysogenum and Aspergillus nidulans. FEBS Lett. 1990 Mar 26;262(2):342-4. PMID:2110531 doi:10.1016/0014-5793(90)80224-7
↑ Tobin MB, Fleming MD, Skatrud PL, Miller JR. Molecular characterization of the acyl-coenzyme A:isopenicillin N acyltransferase gene (penDE) from Penicillium chrysogenum and Aspergillus nidulans and activity of recombinant enzyme in Escherichia coli. J Bacteriol. 1990 Oct;172(10):5908-14. PMID:2120195 doi:10.1128/jb.172.10.5908-5914.1990
↑ Fernández-Aguado M, Ullán RV, Teijeira F, Rodríguez-Castro R, Martín JF. The transport of phenylacetic acid across the peroxisomal membrane is mediated by the PaaT protein in Penicillium chrysogenum. Appl Microbiol Biotechnol. 2013 Apr;97(7):3073-84. PMID:23053082 doi:10.1007/s00253-012-4425-1
↑ Smith DJ, Burnham MK, Edwards J, Earl AJ, Turner G. Cloning and heterologous expression of the penicillin biosynthetic gene cluster from penicillum chrysogenum. Biotechnology (N Y). 1990 Jan;8(1):39-41. PMID:1368505 doi:10.1038/nbt0190-39
↑ Bokhove M, Yoshida H, Hensgens CM, van der Laan JM, Sutherland JD, Dijkstra BW. Structures of an isopenicillin N converting Ntn-hydrolase reveal different catalytic roles for the active site residues of precursor and mature enzyme. Structure. 2010 Mar 10;18(3):301-8. PMID:20223213 doi:10.1016/j.str.2010.01.005

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2x1d"

@@ Line 3: / Line 3: @@
 <StructureSection load='2x1d' size='340' side='right'caption='[[2x1d]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2x1d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_10106 Atcc 10106]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X1D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2x1d]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_chrysogenum Penicillium chrysogenum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X1D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.64&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=D1D:(4S,5S)-1,2-DITHIANE-4,5-DIOL'>D1D</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2x1c|2x1c]], [[2x1e|2x1e]]</div></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Isopenicillin-N_N-acyltransferase Isopenicillin-N N-acyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.164 2.3.1.164] </span></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=2x1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x1d OCA], [https://pdbe.org/2x1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x1d RCSB], [https://www.ebi.ac.uk/pdbsum/2x1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x1d ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/AAAA_PENCH AAAA_PENCH]] Last enzyme in penicillin biosynthetic pathway, which converts isopenicillin N (IPN) to penicillin G, using phenyl-acetyl-CoA or phenoxyacetyl-CoA as acyl donors.
+[https://www.uniprot.org/uniprot/AATA_PENCH AATA_PENCH] Isopenicillin-N N-acyltransferase; part of the gene cluster that mediates the biosynthesis of penicillin, the world's most important antibiotic (PubMed:1368505, PubMed:2110531, PubMed:2120195). AatA catalyzes the exchange of the alpha-aminoadipyl side chain of isopenicillin N for phenylacetic acid to yield penicillin (PubMed:1368505, PubMed:2110531, PubMed:2120195). This step occurs in the peroxisomal matrix and the penM and paaT transporters are involved in the isopenicillin N and phenylacetic acid import into the peroxisome, respectively (PubMed:23053082). 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 aatA to yield penicillin in the peroxisomal matrix (Probable) (PubMed:1368505).<ref>PMID:1368505</ref> <ref>PMID:2110531</ref> <ref>PMID:2120195</ref> <ref>PMID:23053082</ref> <ref>PMID:1368505</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 17: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x1/2x1d_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 35: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 10106]]
-[[Category: Isopenicillin-N N-acyltransferase]]
 [[Category: Large Structures]]
-[[Category: Bokhove, M]]
+[[Category: Penicillium chrysogenum]]
-[[Category: Dijkstra, B W]]
+[[Category: Bokhove M]]
-[[Category: Hensgens, C M.H]]
+[[Category: Dijkstra BW]]
-[[Category: Laan, J M.van der]]
+[[Category: Hensgens CMH]]
-[[Category: Sutherland, J D]]
+[[Category: Sutherland JD]]
-[[Category: Yoshida, H]]
+[[Category: Yoshida H]]
-[[Category: Antibiotic biosynthesis]]
+[[Category: Van der Laan JM]]
-[[Category: Ntn-hydrolase]]
-[[Category: Penicillin biosynthesis]]
-[[Category: Transferase]]
-[[Category: Zymogen]]

2x1d

From Proteopedia

Current revision

The crystal structure of mature acyl coenzyme A:isopenicillin N acyltransferase from Penicillium chrysogenum

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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