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| | <StructureSection load='5k30' size='340' side='right'caption='[[5k30]], [[Resolution|resolution]] 1.59Å' scene=''> | | <StructureSection load='5k30' size='340' side='right'caption='[[5k30]], [[Resolution|resolution]] 1.59Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5k30]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_freundii"_braak_1928 "bacterium freundii" braak 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K30 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K30 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5k30]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Citrobacter_freundii Citrobacter freundii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K30 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.59Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SCS:3-(ETHYLDISULFANYL)-L-ALANINE'>SCS</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SCS:3-(ETHYLDISULFANYL)-L-ALANINE'>SCS</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2rfv|2rfv]]</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=5k30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k30 OCA], [https://pdbe.org/5k30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k30 RCSB], [https://www.ebi.ac.uk/pdbsum/5k30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k30 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AN672_11005, TN42_08855, TO64_18625 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=546 "Bacterium freundii" Braak 1928])</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://proteopedia.org/fgij/fg.htm?mol=5k30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k30 OCA], [http://pdbe.org/5k30 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k30 RCSB], [http://www.ebi.ac.uk/pdbsum/5k30 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k30 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A0A5P8W7_CITFR A0A0A5P8W7_CITFR] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Methionine ó-lyase 3D structures|Methionine ó-lyase 3D structures]] | + | *[[Methionine gamma-lyase 3D structures|Methionine gamma-lyase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacterium freundii braak 1928]] | + | [[Category: Citrobacter freundii]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Methionine gamma-lyase]]
| + | [[Category: Demidkina TV]] |
| - | [[Category: Demidkina, T V]] | + | [[Category: Morozova EA]] |
| - | [[Category: Morozova, E A]] | + | [[Category: Nikulin AD]] |
| - | [[Category: Nikulin, A D]] | + | [[Category: Revtovich SV]] |
| - | [[Category: Revtovich, S V]] | + | |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
5k30 is a 1 chain structure with sequence from Citrobacter freundii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.59Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
A0A0A5P8W7_CITFR
Publication Abstract from PubMed
Interactions of Citrobacter freundii methionine gamma-lyase (MGL) with sulfoxides of typical substrates were investigated. It was found that sulfoxides are suicide substrates of the enzyme. The products of the beta- and gamma-elimination reactions of sulfoxides, thiosulfinates, oxidize three cysteine residues of the enzyme. Three-dimensional structures of MGL inactivated by dimethyl thiosulfinate and diethyl thiosulfinate were determined at 1.46A and 1.59A resolution. Analysis of the structures identified SH groups oxidized by thiosulfinates and revealed the structural bases of MGL inactivation. The extent of inactivation of MGL in the catalysis of the beta-elimination reaction depends on the length of the <<tail>> at oxidized Cys115. Oxidation of Cys115 results in MGL incapable to catalyze the stage of methyl mercaptan elimination of the physiological reaction.
Sulfoxides of sulfur-containing amino acids are suicide substrates of Citrobacter freundii methionine gamma-lyase. Structural bases of the enzyme inactivation.,Revtovich S, Morozova E, Kulikova V, Koval V, Anufrieva N, Nikulin A, Demidkina T Biochimie. 2020 Jan;168:190-197. doi: 10.1016/j.biochi.2019.11.004. Epub 2019 Nov, 9. PMID:31711941[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Revtovich S, Morozova E, Kulikova V, Koval V, Anufrieva N, Nikulin A, Demidkina T. Sulfoxides of sulfur-containing amino acids are suicide substrates of Citrobacter freundii methionine gamma-lyase. Structural bases of the enzyme inactivation. Biochimie. 2020 Jan;168:190-197. doi: 10.1016/j.biochi.2019.11.004. Epub 2019 Nov, 9. PMID:31711941 doi:http://dx.doi.org/10.1016/j.biochi.2019.11.004
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