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3vk4

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Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant complexed with L-homocysteine

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@@ Line 3: / Line 3: @@
 <StructureSection load='3vk4' size='340' side='right'caption='[[3vk4]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3vk4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VK4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3vk4]] 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=3VK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VK4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</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]] 2.61&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2o7c|2o7c]], [[3vk2|3vk2]], [[3vk3|3vk3]]</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=3vk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vk4 OCA], [https://pdbe.org/3vk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vk4 RCSB], [https://www.ebi.ac.uk/pdbsum/3vk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vk4 ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mdeA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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=3vk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vk4 OCA], [http://pdbe.org/3vk4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vk4 RCSB], [http://www.ebi.ac.uk/pdbsum/3vk4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vk4 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/MEGL_PSEPU MEGL_PSEPU]
-Cys116, Lys240&lt;sup&gt;*&lt;/sup&gt;, and Asp241&lt;sup&gt;*&lt;/sup&gt; (asterisks indicate residues from the second subunit of the active dimer) at the active site of L-methionine gamma-lyase of Pseudomonas putida (MGL_Pp) are highly conserved among heterologous MGLs. In a previous study, we found that substitution of Cys116 for His led to a drastic increase in activity toward L-cysteine and a decrease in that toward L-methionine. In this study, we examined some properties of the C116H mutant by kinetic analysis and 3D structural analysis. We assumed that substitution of Cys116 for His broke the original hydrogen-bond network and that this induced a significant effect of Tyr114 as a general acid catalyst, possibly due to the narrow space in the active site. The C116H mutant acquired a novel beta-elimination activity and lead a drastic conformation change in the histidine residue at position 116 by binding the substrate, suggesting that this His residue affects the reaction specificity of C116H. Furthermore, we suggest that Lys240&lt;sup&gt;*&lt;/sup&gt; is important for substrate recognition and structural stability and that Asp241&lt;sup&gt;*&lt;/sup&gt; is also involved in substrate specificity in the elimination reaction. Based on this, we suggest that the hydrogen-bond network among Cys116, Lys240&lt;sup&gt;*&lt;/sup&gt;, and Asp241&lt;sup&gt;*&lt;/sup&gt; contributes to substrate specificity that is, to L-methionine recognition at the active site in MGL_Pp.
-The Role of Amino Acid Residues in the Active Site of &lt;small&gt;L&lt;/small&gt;-Methionine gamma-lyase from &lt;i&gt;Pseudomonas putida&lt;/i&gt;.,Fukumoto M, Kudou D, Murano S, Shiba T, Sato D, Tamura T, Harada S, Inagaki K Biosci Biotechnol Biochem. 2012 Jul 23;76(7):1275-84. Epub 2012 Jul 7. PMID:22785484<ref>PMID:22785484</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3vk4" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Methionine ÃÂ³-lyase 3D structures|Methionine ÃÂ³-lyase 3D structures]]
+*[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus fluorescens putidus flugge 1886]]
 [[Category: Large Structures]]
-[[Category: Methionine gamma-lyase]]
+[[Category: Pseudomonas putida]]
-[[Category: Fukumoto, M]]
+[[Category: Fukumoto M]]
-[[Category: Harada, S]]
+[[Category: Harada S]]
-[[Category: Inagaki, K]]
+[[Category: Inagaki K]]
-[[Category: Kudou, D]]
+[[Category: Kudou D]]
-[[Category: Murano, S]]
+[[Category: Murano S]]
-[[Category: Sato, D]]
+[[Category: Sato D]]
-[[Category: Shiba, T]]
+[[Category: Shiba T]]
-[[Category: Tamura, T]]
+[[Category: Tamura T]]
-[[Category: Lyase]]
-[[Category: Plp]]
-[[Category: Plp-dependent enzyme]]

3vk4

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Current revision

Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant complexed with L-homocysteine

Structural highlights

Function

See Also

Contents

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