3vk4

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<StructureSection load='3vk4' size='340' side='right'caption='[[3vk4]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
<StructureSection load='3vk4' size='340' side='right'caption='[[3vk4]], [[Resolution|resolution]] 2.61&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vk4]] is a 4 chain structure with sequence from [https://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 [https://proteopedia.org/fgij/fg.htm?mol=3VK4 FirstGlance]. <br>
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<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>
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</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></td></tr>
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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]] 2.61&#8491;</td></tr>
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<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>
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<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>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2o7c|2o7c]], [[3vk2|3vk2]], [[3vk3|3vk3]]</div></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mdeA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Methionine_gamma-lyase Methionine gamma-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.4.1.11 4.4.1.11] </span></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=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='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>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/MEGL_PSEPU MEGL_PSEPU]
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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.
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3vk4" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 3D structures]]
*[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus fluorescens putidus flugge 1886]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Methionine gamma-lyase]]
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[[Category: Pseudomonas putida]]
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[[Category: Fukumoto, M]]
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[[Category: Fukumoto M]]
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[[Category: Harada, S]]
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[[Category: Harada S]]
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[[Category: Inagaki, K]]
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[[Category: Inagaki K]]
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[[Category: Kudou, D]]
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[[Category: Kudou D]]
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[[Category: Murano, S]]
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[[Category: Murano S]]
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[[Category: Sato, D]]
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[[Category: Sato D]]
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[[Category: Shiba, T]]
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[[Category: Shiba T]]
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[[Category: Tamura, T]]
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[[Category: Tamura T]]
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[[Category: Lyase]]
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[[Category: Plp]]
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[[Category: Plp-dependent enzyme]]
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Current revision

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

PDB ID 3vk4

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OCA

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