1y2m

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[[Image:1y2m.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of phenylalanine ammonia-lyase from yeast Rhododporidium toruloides==
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|PDB= 1y2m |SIZE=350|CAPTION= <scene name='initialview01'>1y2m</scene>, resolution 1.60&Aring;
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<StructureSection load='1y2m' size='340' side='right'caption='[[1y2m]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>
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<table><tr><td colspan='2'>[[1y2m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodotorula_toruloides Rhodotorula toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y2M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y2M FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Phenylalanine_ammonia-lyase Phenylalanine ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.5 4.3.1.5] </span>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1y2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y2m OCA], [https://pdbe.org/1y2m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y2m RCSB], [https://www.ebi.ac.uk/pdbsum/1y2m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y2m ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1y2m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y2m OCA], [http://www.ebi.ac.uk/pdbsum/1y2m PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1y2m RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/PALY_RHOTO PALY_RHOTO] Catalyzes the non-oxidative deamination of L-phenylalanine and L-tyrosine to form trans-cinnamic acid and p-coumaric acid respectively with similar efficiencies. Facilitates the commitment step in phenylpropanoid pathways that produce lignins, coumarins and flavonoids.<ref>PMID:5102931</ref>
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== Evolutionary Conservation ==
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'''Crystal structure of phenylalanine ammonia-lyase from yeast Rhododporidium toruloides'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/y2/1y2m_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1y2m ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
Structure-based protein engineering coupled with chemical modifications (e.g., pegylation) is a powerful combination to significantly improve the development of proteins as therapeutic agents. As a test case, phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) was selected for enzyme replacement therapy in phenylketonuria [C.R. Scriver, S. Kaufman, Hyperphenylalaninemia:phenylalanine Hydroxylase Deficiency. The Metabolic and Molecular Bases of Inherited Disease, McGraw-Hill, New York, 2001, Chapter 77], an inherited metabolic disorder (OMIM 261600) causing mental retardation due to deficiency of the enzyme l-phenylalanine hydroxylase (EC 1.14.16.1). Previous in vivo studies of recombinant PAL demonstrated a lowering of blood l-phenylalanine levels; yet, the metabolic effect was not sustained due to protein degradation and immunogenicity [C.N. Sarkissian, Z. Shao, F. Blain, R. Peevers, H. Su, R. Heft, T.M. Chang, C.R. Scriver, A different approach to treatment of phenylketonuria:phenylalanine degradation with recombinant phenylalanine ammonia lyase, Proc. Natl. Acad. Sci. USA 96 (1999) 2339; J.A. Hoskins, G. Jack, H.E. Wade, R.J. Peiris, E.C. Wright, D.J. Starr, J. Stern, Enzymatic control of phenylalanine intake in phenylketonuria, Lancet 1 (1980) 392; C.M. Ambrus, S. Anthone, C. Horvath, K. Kalghatgi, A.S. Lele, G. Eapen, J.L. Ambrus, A.J. Ryan, P. Li, Extracorporeal enzyme reactors for depletion of phenylalanine in phenylketonuria, Ann. Intern. Med. 106 (1987) 531]. Here, we report the 1.6A three-dimensional structure of Rhodosporidium toruloides PAL, structure-based molecular engineering, pegylation of PAL, as well as in vitro and in vivo PKU mouse model studies on pegylated PAL formulations. Our results show that pegylation of R. toruloides PAL leads to promising therapeutic efficacy after subcutaneous injection by enhancing the in vivo activity, lowering plasma phenylalanine, and leading to reduced immunogenicity. The three-dimensional structure of PAL provides a basis for understanding the properties of pegylated forms of PAL and strategies for structure-based re-engineering of PAL for PKU treatment.
Structure-based protein engineering coupled with chemical modifications (e.g., pegylation) is a powerful combination to significantly improve the development of proteins as therapeutic agents. As a test case, phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) was selected for enzyme replacement therapy in phenylketonuria [C.R. Scriver, S. Kaufman, Hyperphenylalaninemia:phenylalanine Hydroxylase Deficiency. The Metabolic and Molecular Bases of Inherited Disease, McGraw-Hill, New York, 2001, Chapter 77], an inherited metabolic disorder (OMIM 261600) causing mental retardation due to deficiency of the enzyme l-phenylalanine hydroxylase (EC 1.14.16.1). Previous in vivo studies of recombinant PAL demonstrated a lowering of blood l-phenylalanine levels; yet, the metabolic effect was not sustained due to protein degradation and immunogenicity [C.N. Sarkissian, Z. Shao, F. Blain, R. Peevers, H. Su, R. Heft, T.M. Chang, C.R. Scriver, A different approach to treatment of phenylketonuria:phenylalanine degradation with recombinant phenylalanine ammonia lyase, Proc. Natl. Acad. Sci. USA 96 (1999) 2339; J.A. Hoskins, G. Jack, H.E. Wade, R.J. Peiris, E.C. Wright, D.J. Starr, J. Stern, Enzymatic control of phenylalanine intake in phenylketonuria, Lancet 1 (1980) 392; C.M. Ambrus, S. Anthone, C. Horvath, K. Kalghatgi, A.S. Lele, G. Eapen, J.L. Ambrus, A.J. Ryan, P. Li, Extracorporeal enzyme reactors for depletion of phenylalanine in phenylketonuria, Ann. Intern. Med. 106 (1987) 531]. Here, we report the 1.6A three-dimensional structure of Rhodosporidium toruloides PAL, structure-based molecular engineering, pegylation of PAL, as well as in vitro and in vivo PKU mouse model studies on pegylated PAL formulations. Our results show that pegylation of R. toruloides PAL leads to promising therapeutic efficacy after subcutaneous injection by enhancing the in vivo activity, lowering plasma phenylalanine, and leading to reduced immunogenicity. The three-dimensional structure of PAL provides a basis for understanding the properties of pegylated forms of PAL and strategies for structure-based re-engineering of PAL for PKU treatment.
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==About this Structure==
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Structure-based chemical modification strategy for enzyme replacement treatment of phenylketonuria.,Wang L, Gamez A, Sarkissian CN, Straub M, Patch MG, Han GW, Striepeke S, Fitzpatrick P, Scriver CR, Stevens RC Mol Genet Metab. 2005 Sep-Oct;86(1-2):134-40. Epub 2005 Jul 11. PMID:16006165<ref>PMID:16006165</ref>
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1Y2M is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Y2M OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structure-based chemical modification strategy for enzyme replacement treatment of phenylketonuria., Wang L, Gamez A, Sarkissian CN, Straub M, Patch MG, Han GW, Striepeke S, Fitzpatrick P, Scriver CR, Stevens RC, Mol Genet Metab. 2005 Sep-Oct;86(1-2):134-40. Epub 2005 Jul 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16006165 16006165]
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</div>
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[[Category: Phenylalanine ammonia-lyase]]
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<div class="pdbe-citations 1y2m" style="background-color:#fffaf0;"></div>
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[[Category: Rhodosporidium toruloides]]
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[[Category: Single protein]]
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[[Category: Gamez, A.]]
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[[Category: Han, G W.]]
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[[Category: Patch, M G.]]
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[[Category: Sarkissian, C N.]]
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[[Category: Scriver, C R.]]
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[[Category: Stevens, R C.]]
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[[Category: Straub, M.]]
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[[Category: Wang, L.]]
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[[Category: alpha helice]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:58:00 2008''
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==See Also==
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*[[Aminomutase 3D structures|Aminomutase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Rhodotorula toruloides]]
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[[Category: Gamez A]]
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[[Category: Han GW]]
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[[Category: Patch MG]]
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[[Category: Sarkissian CN]]
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[[Category: Scriver CR]]
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[[Category: Stevens RC]]
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[[Category: Straub M]]
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[[Category: Wang L]]

Current revision

Crystal structure of phenylalanine ammonia-lyase from yeast Rhododporidium toruloides

PDB ID 1y2m

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