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5x30

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==Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates.==
==Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates.==
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<StructureSection load='5x30' size='340' side='right' caption='[[5x30]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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<StructureSection load='5x30' size='340' side='right'caption='[[5x30]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5x30]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X30 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X30 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5x30]] 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=5X30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X30 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4LM:(2E)-2-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}BUT-2-ENOIC+ACID'>4LM</scene>, <scene name='pdbligand=7XF:(2~{S})-2-[[2-METHYL-3-OXIDANYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLAMINO]-4-SULFANYL-BUTANOIC+ACID'>7XF</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <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]] 1.7&#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=4LM:(2E)-2-{[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}BUT-2-ENOIC+ACID'>4LM</scene>, <scene name='pdbligand=7XF:(2~{S})-2-[[2-METHYL-3-OXIDANYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLAMINO]-4-SULFANYL-BUTANOIC+ACID'>7XF</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <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">[[5x2v|5x2v]], [[5x2w|5x2w]], [[5x2x|5x2x]], [[5x2y|5x2y]], [[5x2z|5x2z]]</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=5x30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x30 OCA], [https://pdbe.org/5x30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x30 RCSB], [https://www.ebi.ac.uk/pdbsum/5x30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x30 ProSAT]</span></td></tr>
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<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=5x30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x30 OCA], [http://pdbe.org/5x30 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x30 RCSB], [http://www.ebi.ac.uk/pdbsum/5x30 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x30 ProSAT]</span></td></tr>
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</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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Methionine gamma-lyse (MGL) catalyzes the alpha, gamma-elimination of l-methionine and its derivatives as well as the alpha, beta-elimination of l-cysteine and its derivatives to produce alpha-keto acids, volatile thiols, and ammonia. The reaction mechanism of MGL has been characterized by enzymological studies using several site-directed mutants. The Pseudomonas putida MGL C116H mutant showed drastically reduced degradation activity toward methionine while retaining activity toward homocysteine. To understand the underlying mechanism and to discern the subtle differences between these substrates, we analyzed the crystal structures of the reaction intermediates. The complex formed between the C116H mutant and methionine demonstrated that a loop structure (Ala51-Asn64) in the adjacent subunit of the catalytic dimer cannot approach the cofactor pyridoxal 5'-phosphate (PLP) because His116 disrupts the interaction of Asp241 with Lys240, and the liberated side chain of Lys240 causes steric hindrance with this loop. Conversely, in the complex formed between C116H mutant and homocysteine, the thiol moiety of the substrate conjugated with PLP offsets the imidazole ring of His116 via a water molecule, disrupting the interaction of His116 and Asp241 and restoring the interaction of Asp241 with Lys240. These structural data suggest that the Cys116 to His mutation renders the enzyme inactive toward the original substrate, but activity is restored when the substrate is homocysteine due to substrate-assisted catalysis.
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Structural and mechanistic insights into homocysteine degradation by a mutant of methionine gamma-lyase based on substrate-assisted catalysis.,Sato D, Shiba T, Yunoto S, Furutani K, Fukumoto M, Kudou D, Tamura T, Inagaki K, Harada S Protein Sci. 2017 Mar 22. doi: 10.1002/pro.3158. PMID:28329912<ref>PMID:28329912</ref>
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==See Also==
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*[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 3D structures]]
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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 5x30" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Harada, S]]
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[[Category: Large Structures]]
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[[Category: Sato, D]]
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[[Category: Pseudomonas putida]]
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[[Category: Shiba, T]]
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[[Category: Harada S]]
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[[Category: Lyase]]
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[[Category: Sato D]]
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[[Category: Pyridoxal 5'-phosphate]]
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[[Category: Shiba T]]

Current revision

Crystal structure of Pseudomonas putida methionine gamma-lyase C116H mutant with L-homocysteine intermediates.

PDB ID 5x30

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