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| | <StructureSection load='3czo' size='340' side='right'caption='[[3czo]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='3czo' size='340' side='right'caption='[[3czo]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3czo]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CZO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3CZO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3czo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Trichormus_variabilis Trichormus variabilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CZO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CZO 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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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">[[2nyn|2nyn]]</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>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_ammonia-lyase Histidine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.3 4.3.1.3] </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=3czo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3czo OCA], [https://pdbe.org/3czo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3czo RCSB], [https://www.ebi.ac.uk/pdbsum/3czo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3czo ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3czo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3czo OCA], [http://pdbe.org/3czo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3czo RCSB], [http://www.ebi.ac.uk/pdbsum/3czo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3czo ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PAL_ANAVT PAL_ANAVT]] Catalyzes the non-oxidative deamination of L-phenylalanine to form trans-cinnamic acid, the first step in the phenylpropanoid pathway.<ref>PMID:17240984</ref> <ref>PMID:18556022</ref> | + | [https://www.uniprot.org/uniprot/PAL_TRIV2 PAL_TRIV2] Catalyzes the non-oxidative deamination of L-phenylalanine to form trans-cinnamic acid, the first step in the phenylpropanoid pathway.<ref>PMID:17240984</ref> <ref>PMID:18556022</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cz/3czo_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cz/3czo_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> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Histidine ammonia-lyase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Stevens, R C]] | + | [[Category: Trichormus variabilis]] |
| - | [[Category: Wang, L]] | + | [[Category: Stevens RC]] |
| - | [[Category: Lyase]] | + | [[Category: Wang L]] |
| - | [[Category: Phenylalanine/histidine ammonia-lyase]]
| + | |
| Structural highlights
Function
PAL_TRIV2 Catalyzes the non-oxidative deamination of L-phenylalanine to form trans-cinnamic acid, the first step in the phenylpropanoid pathway.[1] [2]
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
We have recently observed promising success in a mouse model for treating the metabolic disorder phenylketonuria with phenylalanine ammonia lyase (PAL) from Rhodosporidium toruloides and Anabaena variabilis. Both molecules, however, required further optimization in order to overcome problems with protease susceptibility, thermal stability, and aggregation. Previously, we optimized PAL from R. toruloides, and in this case we reduced aggregation of the A. variabilis PAL by mutating two surface cysteine residues (C503 and C565) to serines. Additionally, we report the structural and biochemical characterization of the A. variabilis PAL C503S/C565S double mutant and carefully compare this molecule with the R. toruloides engineered PAL molecule. Unlike previously published PAL structures, significant electron density is observed for the two active-site loops in the A. variabilis C503S/C565S double mutant, yielding a complete view of the active site. Docking studies and N-hydroxysuccinimide-biotin binding studies support a proposed mechanism in which the amino group of the phenylalanine substrate is attacked directly by the 4-methylidene-imidazole-5-one prosthetic group. We propose a helix-to-loop conformational switch in the helices flanking the inner active-site loop that regulates accessibility of the active site. Differences in loop stability among PAL homologs may explain the observed variation in enzyme efficiency, despite the highly conserved structure of the active site. A. variabilis C503S/C565S PAL is shown to be both more thermally stable and more resistant to proteolytic cleavage than R. toruloides PAL. Additional increases in thermal stability and protease resistance upon ligand binding may be due to enhanced interactions among the residues of the active site, possibly locking the active-site structure in place and stabilizing the tetramer. Examination of the A. variabilis C503S/C565S PAL structure, combined with analysis of its physical properties, provides a structural basis for further engineering of residues that could result in a better therapeutic molecule.
Structural and biochemical characterization of the therapeutic Anabaena variabilis phenylalanine ammonia lyase.,Wang L, Gamez A, Archer H, Abola EE, Sarkissian CN, Fitzpatrick P, Wendt D, Zhang Y, Vellard M, Bliesath J, Bell SM, Lemontt JF, Scriver CR, Stevens RC J Mol Biol. 2008 Jul 18;380(4):623-35. Epub 2008 May 17. PMID:18556022[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Moffitt MC, Louie GV, Bowman ME, Pence J, Noel JP, Moore BS. Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and structural characterization. Biochemistry. 2007 Jan 30;46(4):1004-12. PMID:17240984 doi:http://dx.doi.org/10.1021/bi061774g
- ↑ Wang L, Gamez A, Archer H, Abola EE, Sarkissian CN, Fitzpatrick P, Wendt D, Zhang Y, Vellard M, Bliesath J, Bell SM, Lemontt JF, Scriver CR, Stevens RC. Structural and biochemical characterization of the therapeutic Anabaena variabilis phenylalanine ammonia lyase. J Mol Biol. 2008 Jul 18;380(4):623-35. Epub 2008 May 17. PMID:18556022 doi:http://dx.doi.org/10.1016/j.jmb.2008.05.025
- ↑ Wang L, Gamez A, Archer H, Abola EE, Sarkissian CN, Fitzpatrick P, Wendt D, Zhang Y, Vellard M, Bliesath J, Bell SM, Lemontt JF, Scriver CR, Stevens RC. Structural and biochemical characterization of the therapeutic Anabaena variabilis phenylalanine ammonia lyase. J Mol Biol. 2008 Jul 18;380(4):623-35. Epub 2008 May 17. PMID:18556022 doi:http://dx.doi.org/10.1016/j.jmb.2008.05.025
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