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| | ==Crystal structure of the Schiff base intermediate of L-Lys epsilon-oxidase from Marinomonas mediterranea with L-Lys== | | ==Crystal structure of the Schiff base intermediate of L-Lys epsilon-oxidase from Marinomonas mediterranea with L-Lys== |
| - | <StructureSection load='3wev' size='340' side='right' caption='[[3wev]], [[Resolution|resolution]] 1.98Å' scene=''> | + | <StructureSection load='3wev' size='340' side='right'caption='[[3wev]], [[Resolution|resolution]] 1.98Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wev]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Marm1 Marm1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WEV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WEV FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wev]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Marinomonas_mediterranea_MMB-1 Marinomonas mediterranea MMB-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WEV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WEV FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.98Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TRQ:2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC+ACID'>TRQ</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DIO:1,4-DIETHYLENE+DIOXIDE'>DIO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TRQ:2-AMINO-3-(6,7-DIOXO-6,7-DIHYDRO-1H-INDOL-3-YL)-PROPIONIC+ACID'>TRQ</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3weu|3weu]]</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=3wev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wev OCA], [https://pdbe.org/3wev PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wev RCSB], [https://www.ebi.ac.uk/pdbsum/3wev PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wev ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lodA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=717774 MARM1])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lysine_6-oxidase L-lysine 6-oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.20 1.4.3.20] </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=3wev FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wev OCA], [http://pdbe.org/3wev PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wev RCSB], [http://www.ebi.ac.uk/pdbsum/3wev PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wev ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LODA_MARM1 LODA_MARM1]] Has antibacterial activity against a wide spectrum of Gram-positive and Gram-negative bacteria including nosocomial isolates of S.aureus and Pseudomonas sp. The antimicrobial activity is due to hydrogen peroxide generated by its lysine oxidase activity. Also has autotoxic activity. Involved in biofilm differentiation; responsible for cell death within microcolonies during biofilm development which is linked to the generation of a phenotypically diverse dispersal population and thus may play a role in colonization.<ref>PMID:15652194</ref> <ref>PMID:18502869</ref> <ref>PMID:20025674</ref> | + | [https://www.uniprot.org/uniprot/LODA_MARM1 LODA_MARM1] Has antibacterial activity against a wide spectrum of Gram-positive and Gram-negative bacteria including nosocomial isolates of S.aureus and Pseudomonas sp. The antimicrobial activity is due to hydrogen peroxide generated by its lysine oxidase activity. Also has autotoxic activity. Involved in biofilm differentiation; responsible for cell death within microcolonies during biofilm development which is linked to the generation of a phenotypically diverse dispersal population and thus may play a role in colonization.<ref>PMID:15652194</ref> <ref>PMID:18502869</ref> <ref>PMID:20025674</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: L-lysine 6-oxidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Marm1]] | + | [[Category: Marinomonas mediterranea MMB-1]] |
| - | [[Category: Akaji, S]] | + | [[Category: Akaji S]] |
| - | [[Category: Asano, Y]] | + | [[Category: Asano Y]] |
| - | [[Category: Inagaki, K]] | + | [[Category: Inagaki K]] |
| - | [[Category: Matsui, D]] | + | [[Category: Matsui D]] |
| - | [[Category: Nakano, S]] | + | [[Category: Nakano S]] |
| - | [[Category: Okazaki, S]] | + | [[Category: Okazaki S]] |
| - | [[Category: Amine oxidase]]
| + | |
| - | [[Category: Amino acid oxidase]]
| + | |
| - | [[Category: Arm]]
| + | |
| - | [[Category: Beta barrel]]
| + | |
| - | [[Category: L-lys binding]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Three be-ta sheet]]
| + | |
| Structural highlights
3wev is a 2 chain structure with sequence from Marinomonas mediterranea MMB-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.98Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
LODA_MARM1 Has antibacterial activity against a wide spectrum of Gram-positive and Gram-negative bacteria including nosocomial isolates of S.aureus and Pseudomonas sp. The antimicrobial activity is due to hydrogen peroxide generated by its lysine oxidase activity. Also has autotoxic activity. Involved in biofilm differentiation; responsible for cell death within microcolonies during biofilm development which is linked to the generation of a phenotypically diverse dispersal population and thus may play a role in colonization.[1] [2] [3]
Publication Abstract from PubMed
We have determined the x-ray crystal structure of l-lysine epsilon-oxidase from Marinomonas mediterranea in its native and l-lysine-complex forms at 1.94- and 1.99-A resolution, respectively. In the native enzyme, electron densities clearly indicate the presence of cysteine tryptophylquinone (CTQ) previously identified in quinohemoprotein amine dehydrogenase. In the l-lysine-complex, an electron density corresponding to the bound l-lysine shows that its epsilon-amino group is attached to the C6 carbonyl group of CTQ, suggesting the formation of a Schiff-base intermediate. Collectively, the present crystal structure provides the first example of an enzyme employing a tryptophylquinone cofactor in an amine oxidase.
X-Ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine {varepsilon}-oxidase from Marinomonas mediterranea.,Okazaki S, Nakano S, Matsui D, Akaji S, Inagaki K, Asano Y J Biochem. 2013 Sep;154(3):233-6. doi: 10.1093/jb/mvt070. Epub 2013 Aug 1. PMID:23908359[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lucas-Elio P, Hernandez P, Sanchez-Amat A, Solano F. Purification and partial characterization of marinocine, a new broad-spectrum antibacterial protein produced by Marinomonas mediterranea. Biochim Biophys Acta. 2005 Jan 18;1721(1-3):193-203. Epub 2004 Nov 26. PMID:15652194 doi:http://dx.doi.org/10.1016/j.bbagen.2004.11.002
- ↑ Mai-Prochnow A, Lucas-Elio P, Egan S, Thomas T, Webb JS, Sanchez-Amat A, Kjelleberg S. Hydrogen peroxide linked to lysine oxidase activity facilitates biofilm differentiation and dispersal in several gram-negative bacteria. J Bacteriol. 2008 Aug;190(15):5493-501. doi: 10.1128/JB.00549-08. Epub 2008 May, 23. PMID:18502869 doi:http://dx.doi.org/10.1128/JB.00549-08
- ↑ Gomez D, Lucas-Elio P, Solano F, Sanchez-Amat A. Both genes in the Marinomonas mediterranea lodAB operon are required for the expression of the antimicrobial protein lysine oxidase. Mol Microbiol. 2010 Jan;75(2):462-73. doi: 10.1111/j.1365-2958.2009.07000.x. Epub, 2009 Dec 16. PMID:20025674 doi:http://dx.doi.org/10.1111/j.1365-2958.2009.07000.x
- ↑ Okazaki S, Nakano S, Matsui D, Akaji S, Inagaki K, Asano Y. X-Ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine {varepsilon}-oxidase from Marinomonas mediterranea. J Biochem. 2013 Sep;154(3):233-6. doi: 10.1093/jb/mvt070. Epub 2013 Aug 1. PMID:23908359 doi:10.1093/jb/mvt070
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