3vk3: Difference between revisions
New page: '''Unreleased structure''' The entry 3vk3 is ON HOLD Authors: Fukumoto, M., Kudou, D., Murano, S., Shiba, T., Sato, D., Tamura, T., Harada, S., Inagaki, K. Description: Crystal Structu... |
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The | ==Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant Complexed with L-methionine== | ||
<StructureSection load='3vk3' size='340' side='right'caption='[[3vk3]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3vk3]] 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=3VK3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VK3 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> | |||
<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=MET:METHIONINE'>MET</scene></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=3vk3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vk3 OCA], [https://pdbe.org/3vk3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vk3 RCSB], [https://www.ebi.ac.uk/pdbsum/3vk3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vk3 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/MEGL_PSEPU MEGL_PSEPU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Cys116, Lys240<sup>*</sup>, and Asp241<sup>*</sup> (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<sup>*</sup> is important for substrate recognition and structural stability and that Asp241<sup>*</sup> is also involved in substrate specificity in the elimination reaction. Based on this, we suggest that the hydrogen-bond network among Cys116, Lys240<sup>*</sup>, and Asp241<sup>*</sup> 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 <small>L</small>-Methionine gamma-lyase from <i>Pseudomonas putida</i>.,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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3vk3" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pseudomonas putida]] | |||
[[Category: Fukumoto M]] | |||
[[Category: Harada S]] | |||
[[Category: Inagaki K]] | |||
[[Category: Kudou D]] | |||
[[Category: Murano S]] | |||
[[Category: Sato D]] | |||
[[Category: Shiba T]] | |||
[[Category: Tamura T]] | |||
Latest revision as of 15:24, 8 November 2023
Crystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant Complexed with L-methionineCrystal Structure of L-Methionine gamma-Lyase from Pseudomonas putida C116H Mutant Complexed with L-methionine
Structural highlights
FunctionPublication Abstract from PubMedCys116, Lys240<sup>*</sup>, and Asp241<sup>*</sup> (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<sup>*</sup> is important for substrate recognition and structural stability and that Asp241<sup>*</sup> is also involved in substrate specificity in the elimination reaction. Based on this, we suggest that the hydrogen-bond network among Cys116, Lys240<sup>*</sup>, and Asp241<sup>*</sup> 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 <small>L</small>-Methionine gamma-lyase from <i>Pseudomonas putida</i>.,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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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