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| | <StructureSection load='6icn' size='340' side='right'caption='[[6icn]], [[Resolution|resolution]] 1.65Å' scene=''> | | <StructureSection load='6icn' size='340' side='right'caption='[[6icn]], [[Resolution|resolution]] 1.65Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6icn]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ICN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ICN FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6icn]] is a 3 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=6ICN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ICN FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndmA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CFF:CAFFEINE'>CFF</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methylxanthine_N(1)-demethylase Methylxanthine N(1)-demethylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.14.13.178 1.14.13.178] </span></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=6icn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6icn OCA], [https://pdbe.org/6icn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6icn RCSB], [https://www.ebi.ac.uk/pdbsum/6icn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6icn ProSAT]</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=6icn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6icn OCA], [http://pdbe.org/6icn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6icn RCSB], [http://www.ebi.ac.uk/pdbsum/6icn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6icn ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NDMA_PSEPU NDMA_PSEPU]] Involved in the caffeine degradation, which is the essential first step for assimilating the carbon and nitrogen in caffeine. Catalyzes the N1-demethylation of caffeine to produce theobromine and formaldehyde. Also catalyzes the N1-demethylation of theophylline, paraxanthine, and 1-methylxanthine to 3-methylxanthine, 7-methylxanthine, and xanthine, respectively. NADH is the preferred substrate.<ref>PMID:20966097</ref> <ref>PMID:22328667</ref> | + | [https://www.uniprot.org/uniprot/NDMA_PSEPU NDMA_PSEPU] Involved in the caffeine degradation, which is the essential first step for assimilating the carbon and nitrogen in caffeine. Catalyzes the N1-demethylation of caffeine to produce theobromine and formaldehyde. Also catalyzes the N1-demethylation of theophylline, paraxanthine, and 1-methylxanthine to 3-methylxanthine, 7-methylxanthine, and xanthine, respectively. NADH is the preferred substrate.<ref>PMID:20966097</ref> <ref>PMID:22328667</ref> |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | Caffeine, found in many foods, beverages, and pharmaceuticals, is the most used chemical compound for mental alertness. It is originally a natural product of plants and exists widely in environmental soil. Some bacteria, such as Pseudomonas putida CBB5, utilize caffeine as a sole carbon and nitrogen source by degrading it through sequential N-demethylation catalyzed by five enzymes (NdmA, NdmB, NdmC, NdmD, and NdmE). The environmentally friendly enzymatic reaction products, methylxanthines, are high-value biochemicals that are used in the pharmaceutical and cosmetic industries. However, the structures and biochemical properties of bacterial N-demethylases remain largely unknown. Here, we report the structures of NdmA and NdmB, the initial N1- and N3-specific demethylases, respectively. Reverse-oriented substrate bindings were observed in the substrate-complexed structures, offering methyl position specificity for proper N-demethylation. For efficient sequential degradation of caffeine, these enzymes form a unique heterocomplex with 3:3 stoichiometry, which was confirmed by enzymatic assays, fluorescent labeling, and small-angle x-ray scattering. The binary structure of NdmA with the ferredoxin domain of NdmD, which is the first structural information for the plant-type ferredoxin domain in a complex state, was also determined to better understand electron transport during N-demethylation. These findings broaden our understanding of the caffeine degradation mechanism by bacterial enzymes and will enable their use for industrial applications.
| + | |
| - | | + | |
| - | Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.,Kim JH, Kim BH, Brooks S, Kang SY, Summers RM, Song HK J Mol Biol. 2019 Sep 6;431(19):3647-3661. doi: 10.1016/j.jmb.2019.08.004. Epub, 2019 Aug 11. PMID:31412262<ref>PMID:31412262</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 6icn" style="background-color:#fffaf0;"></div>
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus fluorescens putidus flugge 1886]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kang, S Y]] | + | [[Category: Pseudomonas putida]] |
| - | [[Category: Kim, B H]] | + | [[Category: Kang SY]] |
| - | [[Category: Kim, J H]] | + | [[Category: Kim BH]] |
| - | [[Category: Song, H K]] | + | [[Category: Kim JH]] |
| - | [[Category: Caffeine degradation]] | + | [[Category: Song HK]] |
| - | [[Category: Metal binding protein]]
| + | |
| - | [[Category: N-demethylase]]
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| - | [[Category: Non-heme iron center]]
| + | |
| - | [[Category: Rieske oxygenase]]
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