2o7c

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(New page: 200px<br /><applet load="2o7c" size="350" color="white" frame="true" align="right" spinBox="true" caption="2o7c, resolution 1.7&Aring;" /> '''Crystal structure of ...)
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[[Image:2o7c.jpg|left|200px]]<br /><applet load="2o7c" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2o7c, resolution 1.7&Aring;" />
 
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'''Crystal structure of L-methionine-lyase from Pseudomonas'''<br />
 
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==Overview==
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==Crystal structure of L-methionine-lyase from Pseudomonas==
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l-Methionine gamma-lyase (EC 4.4.1.11, MGL_Pp) from Pseudomonas putida is, a multifunctional enzyme, which belongs to the gamma-family of, pyridoxal-5'-phosphate (PLP) dependent enzymes. In this report, we, demonstrate that the three-dimensional structure of MGL_Pp has been, completely solved by the molecular replacement method to an R-factor of, 20.4% at 1.8 A resolution. Detailed information of the overall structure, of MGL_Pp supplies a clear picture of the substrate- and PLP-binding, pockets. Tyr59 and Arg61 of neighbouring subunits, which are strongly, conserved in other gamma-family enzymes, contact the phosphate group of, PLP. These residues are important as the main anchor within the active, site. Lys240, Asp241 and Arg61 of one partner monomer and Tyr114 and, Cys116 of the other partner monomer form a hydrogen-bond network in the, MGL active site which is specific for MGLs. It is also suggested that, electrostatic interactions at the subunit interface are involved in the, stabilization of the structural conformation. The detailed structure will, facilitate the development of MGL_Pp as an anticancer drug.
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<StructureSection load='2o7c' size='340' side='right'caption='[[2o7c]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2o7c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2O7C FirstGlance]. <br>
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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]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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=2o7c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2o7c OCA], [https://pdbe.org/2o7c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2o7c RCSB], [https://www.ebi.ac.uk/pdbsum/2o7c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2o7c ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MEGL_PSEPU MEGL_PSEPU]
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== Evolutionary Conservation ==
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o7/2o7c_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2o7c 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 ==
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l-Methionine gamma-lyase (EC 4.4.1.11, MGL_Pp) from Pseudomonas putida is a multifunctional enzyme, which belongs to the gamma-family of pyridoxal-5'-phosphate (PLP) dependent enzymes. In this report, we demonstrate that the three-dimensional structure of MGL_Pp has been completely solved by the molecular replacement method to an R-factor of 20.4% at 1.8 A resolution. Detailed information of the overall structure of MGL_Pp supplies a clear picture of the substrate- and PLP-binding pockets. Tyr59 and Arg61 of neighbouring subunits, which are strongly conserved in other gamma-family enzymes, contact the phosphate group of PLP. These residues are important as the main anchor within the active site. Lys240, Asp241 and Arg61 of one partner monomer and Tyr114 and Cys116 of the other partner monomer form a hydrogen-bond network in the MGL active site which is specific for MGLs. It is also suggested that electrostatic interactions at the subunit interface are involved in the stabilization of the structural conformation. The detailed structure will facilitate the development of MGL_Pp as an anticancer drug.
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==About this Structure==
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Structure of the antitumour enzyme L-methionine gamma-lyase from Pseudomonas putida at 1.8 A resolution.,Kudou D, Misaki S, Yamashita M, Tamura T, Takakura T, Yoshioka T, Yagi S, Hoffman RM, Takimoto A, Esaki N, Inagaki K J Biochem. 2007 Apr;141(4):535-44. Epub 2007 Feb 8. PMID:17289792<ref>PMID:17289792</ref>
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2O7C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Methionine_gamma-lyase Methionine gamma-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.11 4.4.1.11] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2O7C 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 of the antitumour enzyme L-methionine gamma-lyase from Pseudomonas putida at 1.8 A resolution., Kudou D, Misaki S, Yamashita M, Tamura T, Takakura T, Yoshioka T, Yagi S, Hoffman RM, Takimoto A, Esaki N, Inagaki K, J Biochem (Tokyo). 2007 Apr;141(4):535-44. Epub 2007 Feb 8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17289792 17289792]
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</div>
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[[Category: Methionine gamma-lyase]]
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<div class="pdbe-citations 2o7c" style="background-color:#fffaf0;"></div>
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[[Category: Pseudomonas putida]]
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[[Category: Single protein]]
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[[Category: Inagaki, K.]]
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[[Category: Misaki, S.]]
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[[Category: Takakura, T.]]
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[[Category: Takimoto, A.]]
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[[Category: Tamura, T.]]
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[[Category: Tanaka, H.]]
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[[Category: Yamashita, M.]]
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[[Category: Yoshioka, T.]]
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[[Category: SO4]]
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[[Category: cancer]]
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[[Category: lyase]]
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[[Category: methionine]]
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[[Category: plp]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:43:11 2008''
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==See Also==
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*[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 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: Pseudomonas putida]]
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[[Category: Inagaki K]]
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[[Category: Misaki S]]
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[[Category: Takakura T]]
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[[Category: Takimoto A]]
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[[Category: Tamura T]]
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[[Category: Tanaka H]]
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[[Category: Yamashita M]]
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[[Category: Yoshioka T]]

Current revision

Crystal structure of L-methionine-lyase from Pseudomonas

PDB ID 2o7c

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