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- SASDFG7: Pseudomonas putida CBB5 NdmB hexamer (Methylxanthine N3-demethyla... -
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Open data
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Basic information
Entry | Database: SASBDB / ID: SASDFG7 |
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![]() | Pseudomonas putida CBB5 NdmB hexamer
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Function / homology | ![]() methylxanthine N3-demethylase / alkaloid catabolic process / demethylase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding / cytoplasm Similarity search - Function |
Biological species | ![]() |
![]() | ![]() Title: Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex. Authors: Jun Hoe Kim / Bong Heon Kim / Shelby Brooks / Seung Yeon Kang / Ryan M Summers / Hyun Kyu Song / ![]() ![]() Abstract: 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 ...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 N- and N-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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
-Data source
SASBDB page | ![]() |
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-Related structure data
Related structure data | ![]() 6ickC ![]() 6iclC ![]() 6icmC ![]() 6icnC ![]() 6icoC ![]() 6icpC ![]() 6icqC C: citing same article ( |
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Similar structure data |
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External links
Related items in Molecule of the Month |
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-Models
Model #3136 | ![]() Type: dummy / Radius of dummy atoms: 4.00 A / Symmetry: P3 / Chi-square value: 0.959 / P-value: 0.294224 ![]() |
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Sample
![]() | Name: Pseudomonas putida CBB5 NdmB hexamer / Specimen concentration: 9.7 mg/ml |
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Buffer | Name: 20 mM HEPES 150 mM NaCl 2 mM TCEP / pH: 7.5 / Comment: gel filtration buffer |
Entity #1713 | Type: protein / Description: Methylxanthine N3-demethylase NdmB / Formula weight: 43.012 / Num. of mol.: 6 / Source: Pseudomonas putida / References: UniProt: H9N290 Sequence: MGSSHHHHHH ENLYFQGSMK EQLKPLLEDK TYLRHFWHPV CTLNEFERAN ASGHGPMGVT LLGEKLVLAR LNSKIIAAAD RCAHRSAQLS IGRVCSNAGK DYLECPYHGW RYDEAGACQL IPACPDKSIS PRAKISSFDC EVKYDIVWVR LDNSFDCTQI PYLSDFDNPD ...Sequence: MGSSHHHHHH ENLYFQGSMK EQLKPLLEDK TYLRHFWHPV CTLNEFERAN ASGHGPMGVT LLGEKLVLAR LNSKIIAAAD RCAHRSAQLS IGRVCSNAGK DYLECPYHGW RYDEAGACQL IPACPDKSIS PRAKISSFDC EVKYDIVWVR LDNSFDCTQI PYLSDFDNPD MQVIVADSYI WETVAERRWE NFTDFSHFAF VHPGTLYDPF FASHPTVYVN RVDGELQFKL APPREMKGIP PEAPMGDFTY RCTMPYSVNL EIKLWKDDSR FVLWTTASPV DNKSCRNFMI IVREKDNQPD HMHLAFQKRV LDEDQPVIES QWPLEIQTSE VSVATDKISV QFRKWHKELS LSAVEGREAF RDSVLTNVIE EEQ |
-Experimental information
Beam | Instrument name: Photon Factory (PF), High Energy Accelerator Research Organization (KEK) BL-10C City: Tsukuba / 国: Japan ![]() | ||||||||||||||||||
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Detector | Name: Pilatus3 2M / Pixsize x: 0.172 mm | ||||||||||||||||||
Scan |
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Distance distribution function P(R) |
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Result |
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