View source for 6icm


==Pseudomonas putida CBB5 NdmA with ferredoxin domain of NdmD==
<StructureSection load='6icm' size='340' side='right'caption='[[6icm]], [[Resolution|resolution]] 2.96&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6icm]] 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=6ICM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ICM FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.961&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></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=6icm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6icm OCA], [https://pdbe.org/6icm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6icm RCSB], [https://www.ebi.ac.uk/pdbsum/6icm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6icm ProSAT]</span></td></tr>
</table>
== Function ==
[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>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6icm" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas putida]]
[[Category: Kang SY]]
[[Category: Kim BH]]
[[Category: Kim JH]]
[[Category: Song HK]]