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| | ==Methionine gamma-lyase from Citrobacter freundii with pyridoximine-5'-phosphate== | | ==Methionine gamma-lyase from Citrobacter freundii with pyridoximine-5'-phosphate== |
| - | <StructureSection load='3mkj' size='340' side='right' caption='[[3mkj]], [[Resolution|resolution]] 1.65Å' scene=''> | + | <StructureSection load='3mkj' size='340' side='right'caption='[[3mkj]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3mkj]] 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=3MKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MKJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3mkj]] 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=3MKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MKJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PZP:[5-HYDROXY-4-(IMINOMETHYL)-6-METHYL-PYRIDIN-3-YL]METHYL+DIHYDROGEN+PHOSPHATE'>PZP</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]] 1.65Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=PZP:[5-HYDROXY-4-(IMINOMETHYL)-6-METHYL-PYRIDIN-3-YL]METHYL+DIHYDROGEN+PHOSPHATE'>PZP</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2rfv|2rfv]], [[1y4i|1y4i]], [[3jwb|3jwb]], [[3jwa|3jwa]], [[3jw9|3jw9]]</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=3mkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mkj OCA], [https://pdbe.org/3mkj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mkj RCSB], [https://www.ebi.ac.uk/pdbsum/3mkj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mkj ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">megL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=546 "Bacterium freundii" Braak 1928])</td></tr>
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| - | <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=3mkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mkj OCA], [http://pdbe.org/3mkj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3mkj RCSB], [http://www.ebi.ac.uk/pdbsum/3mkj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3mkj ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q84AR1_CITFR Q84AR1_CITFR] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mk/3mkj_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mk/3mkj_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | ==See Also== | | ==See Also== |
| - | *[[Methionine gamma-lyase|Methionine gamma-lyase]] | + | *[[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: Methionine gamma-lyase]] | + | [[Category: Large Structures]] |
| - | [[Category: Demidkina, T V]] | + | [[Category: Demidkina TV]] |
| - | [[Category: Morozova, E A]] | + | [[Category: Morozova EA]] |
| - | [[Category: Nikulin, A D]] | + | [[Category: Nikulin AD]] |
| - | [[Category: Revtovich, S V]] | + | [[Category: Revtovich SV]] |
| - | [[Category: Lyase]]
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| - | [[Category: Plp-dependent enzyme]]
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| - | [[Category: Pyridoxal-5'-phosphate]]
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| - | [[Category: X-ray damage]]
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| Structural highlights
Function
Q84AR1_CITFR
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Pyridoxal 5'-phosphate (PLP) dependent methionine gamma-lyase catalyzes the breakdown of L-methionine to alpha-ketobutyric acid, methanethiol and ammonia. This enzyme, present in anaerobic microorganisms, has biomedical interest both for its activity as antitumor agent, depleting methionine supply in methionine-dependent cancers, and as target in the treatment of human pathogen infections, activating the pro-drug trifluoromethionine. To validate the structure of the enzyme from Citrobacter freundii, crystallized from monomethyl ether polyethylene glycol 2000, for the development of lead compounds, the reactivity of the crystalline enzyme towards L-methionine, substrate analogs and inhibitors was determined by polarized absorption microspectrophotometry. Spectral data were also collected for enzyme crystals, grown in monomethyl ether polyethylene glycol 2000 in the presence of ammonium sulfate. The three-dimensional structure of these enzyme crystals, solved at 1.65A resolution with R(free) 23.2%, revealed the surprising absence of the aldimine bond between the active site Lys210 and PLP. Different hypothesis are proposed and discussed in the light of spectral and structural data, pointing out to the relevance of the complementarity between X-ray crystallography and single crystal spectroscopy for the understanding of biological mechanisms at molecular level.
Exploring methionine gamma-lyase structure-function relationship via microspectrophotometry and X-ray crystallography.,Ronda L, Bazhulina NP, Morozova EA, Revtovich SV, Chekhov VO, Nikulin AD, Demidkina TV, Mozzarelli A Biochim Biophys Acta. 2010 Jul 1. PMID:20601224[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ronda L, Bazhulina NP, Morozova EA, Revtovich SV, Chekhov VO, Nikulin AD, Demidkina TV, Mozzarelli A. Exploring methionine gamma-lyase structure-function relationship via microspectrophotometry and X-ray crystallography. Biochim Biophys Acta. 2010 Jul 1. PMID:20601224 doi:10.1016/j.bbapap.2010.06.017
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