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| | ==Ironing out their differences: Dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase== | | ==Ironing out their differences: Dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase== |
| - | <StructureSection load='4v2r' size='340' side='right' caption='[[4v2r]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='4v2r' size='340' side='right'caption='[[4v2r]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4v2r]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chinese_yew Chinese yew]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4V2R FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4v2r]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Taxus_chinensis Taxus chinensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V2R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V2R FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MDO:{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>MDO</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">[[4v2q|4v2q]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MDO:{2-[(1S)-1-AMINOETHYL]-4-METHYLIDENE-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>MDO</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4v2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2r OCA], [http://pdbe.org/4v2r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4v2r RCSB], [http://www.ebi.ac.uk/pdbsum/4v2r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2r ProSAT]</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=4v2r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v2r OCA], [https://pdbe.org/4v2r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v2r RCSB], [https://www.ebi.ac.uk/pdbsum/4v2r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v2r ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PAM_TAXWC PAM_TAXWC]] Phenylalanine aminomutase that catalyzes the rearrangement of L-phenylalanine to R-beta-phenylalanine. Catalyzes the first commited step in the biosynthesis of the side chain of the alkaloid taxol (paclitaxel), a widely-used compound with antitumor activity. Has also low phenylalanine ammonia-lyase activity and can catalyze the amination of trans-cinnamate.<ref>PMID:15878763</ref> <ref>PMID:22113970</ref> <ref>PMID:24786474</ref> | + | [https://www.uniprot.org/uniprot/PAM_TAXWC PAM_TAXWC] Phenylalanine aminomutase that catalyzes the rearrangement of L-phenylalanine to R-beta-phenylalanine. Catalyzes the first commited step in the biosynthesis of the side chain of the alkaloid taxol (paclitaxel), a widely-used compound with antitumor activity. Has also low phenylalanine ammonia-lyase activity and can catalyze the amination of trans-cinnamate.<ref>PMID:15878763</ref> <ref>PMID:22113970</ref> <ref>PMID:24786474</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Aminomutase|Aminomutase]] | + | *[[Aminomutase 3D structures|Aminomutase 3D structures]] |
| - | *[[Ubiquitin protein ligase|Ubiquitin protein ligase]] | + | *[[Ubiquitin protein ligase 3D structures|Ubiquitin protein ligase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Chinese yew]] | + | [[Category: Large Structures]] |
| - | [[Category: Bartsch, S]] | + | [[Category: Taxus chinensis]] |
| - | [[Category: Dijkstra, B W]] | + | [[Category: Bartsch S]] |
| - | [[Category: Heberling, M]] | + | [[Category: Dijkstra BW]] |
| - | [[Category: Janssen, D]] | + | [[Category: Heberling M]] |
| - | [[Category: Marrink, S]] | + | [[Category: Janssen D]] |
| - | [[Category: Masman, M]] | + | [[Category: Marrink S]] |
| - | [[Category: Wybenga, G G]] | + | [[Category: Masman M]] |
| - | [[Category: Lyase]]
| + | [[Category: Wybenga GG]] |
| Structural highlights
Function
PAM_TAXWC Phenylalanine aminomutase that catalyzes the rearrangement of L-phenylalanine to R-beta-phenylalanine. Catalyzes the first commited step in the biosynthesis of the side chain of the alkaloid taxol (paclitaxel), a widely-used compound with antitumor activity. Has also low phenylalanine ammonia-lyase activity and can catalyze the amination of trans-cinnamate.[1] [2] [3]
Publication Abstract from PubMed
Deciphering the structural features that functionally separate ammonia lyases from aminomutases is of interest because it may allow for the engineering of more efficient aminomutases for the synthesis of unnatural amino acids (e.g., beta-amino acids). However, this has proved to be a major challenge that involves understanding the factors that influence their activity and regioselectivity differences. Herein, we report evidence of a structural determinant that dictates the activity differences between a phenylalanine ammonia lyase (PAL) and aminomutase (PAM). An inner loop region that closes the active sites of both PAM and PAL was mutated within PAM (PAM residues 77-97) in a step-wise approach to study the effects when the equivalent residue(s) found in the PAL loop were introduced into the PAM loop. Almost all of the single loop mutations triggered a lyase phenotype in PAM. Experimental and computational evidence suggest that the induced lyase features result from inner loop mobility enhancements, which are possibly caused by a 310-helix cluster, flanking alpha-helices, and hydrophobic interactions. These findings pinpoint the inner loop as a structural determinant of the lyase and mutase activities of PAM.
Ironing out their differences: Dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase.,Heberling MM, Masman MF, Bartsch S, Wybenga GG, Dijkstra BW, Marrink SJ, Janssen DB ACS Chem Biol. 2014 Dec 10. PMID:25494407[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Steele CL, Chen Y, Dougherty BA, Li W, Hofstead S, Lam KS, Xing Z, Chiang SJ. Purification, cloning, and functional expression of phenylalanine aminomutase: the first committed step in Taxol side-chain biosynthesis. Arch Biochem Biophys. 2005 Jun 1;438(1):1-10. PMID:15878763 doi:http://dx.doi.org/10.1016/j.abb.2005.04.012
- ↑ Wu B, Szymanski W, Wybenga GG, Heberling MM, Bartsch S, de Wildeman S, Poelarends GJ, Feringa BL, Dijkstra BW, Janssen DB. Mechanism-inspired engineering of phenylalanine aminomutase for enhanced beta-regioselective asymmetric amination of cinnamates. Angew Chem Int Ed Engl. 2012 Jan 9;51(2):482-6. doi: 10.1002/anie.201106372. Epub, 2011 Nov 23. PMID:22113970 doi:http://dx.doi.org/10.1002/anie.201106372
- ↑ Wybenga GG, Szymanski W, Wu B, Feringa BL, Janssen DB, Dijkstra BW. Structural Investigations into the Stereochemistry and Activity of a Phenylalanine-2,3-aminomutase from Taxus chinensis. Biochemistry. 2014 May 12. PMID:24786474 doi:http://dx.doi.org/10.1021/bi500187a
- ↑ Heberling MM, Masman MF, Bartsch S, Wybenga GG, Dijkstra BW, Marrink SJ, Janssen DB. Ironing out their differences: Dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase. ACS Chem Biol. 2014 Dec 10. PMID:25494407 doi:http://dx.doi.org/10.1021/cb500794h
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