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Yorodumi- SASDFF7: Pseudomonas putida CBB5 NdmA hexamer (Methylxanthine N1-demethyla... -
+Open data
-Basic information
Entry | Database: SASBDB / ID: SASDFF7 |
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Sample | Pseudomonas putida CBB5 NdmA hexamer
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Function / homology | Function and homology information methylxanthine N1-demethylase / alkaloid catabolic process / demethylase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding Similarity search - Function |
Biological species | Pseudomonas putida (bacteria) |
Citation | Journal: J Mol Biol / Year: 2019 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. |
Contact author |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Data source
SASBDB page | SASDFF7 |
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-Related structure data
Related structure data | 6ickC 6iclC 6icmC 6icnC 6icoC 6icpC 6icqC C: citing same article (ref.) |
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Similar structure data |
-External links
Related items in Molecule of the Month |
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-Models
Model #3135 | Type: dummy / Radius of dummy atoms: 3.75 A / Symmetry: P3 / Chi-square value: 1.161 / P-value: 0.010778 Search similar-shape structures of this assembly by Omokage search (details) |
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-Sample
Sample | Name: Pseudomonas putida CBB5 NdmA hexamer / Specimen concentration: 12.1 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 #1712 | Type: protein / Description: Methylxanthine N1-demethylase NdmA / Formula weight: 42.327 / Num. of mol.: 6 / Source: Pseudomonas putida / References: UniProt: H9N289 Sequence: MGSSHHHHHH ENLYFQGSME QAIINDEREY LRHFWHPVCT VTELEKAHPS SLGPLAVKLL NEQLVVAKLG DEYVAMRDRC AHRSAKLSLG TVSGNRLQCP YHGWQYDTHG ACQLVPACPN SPIPNKAKVD RFDCEERYGL IWIRLDSSFD CTEIPYFSAA NDPRLRIVIQ ...Sequence: MGSSHHHHHH ENLYFQGSME QAIINDEREY LRHFWHPVCT VTELEKAHPS SLGPLAVKLL NEQLVVAKLG DEYVAMRDRC AHRSAKLSLG TVSGNRLQCP YHGWQYDTHG ACQLVPACPN SPIPNKAKVD RFDCEERYGL IWIRLDSSFD CTEIPYFSAA NDPRLRIVIQ EPYWWDATAE RRWENFTDFS HFAFIHPGTL FDPNNAEPPI VPMDRFNGQF RFVYDTPEDM AVPNQAPIGS FSYTCSMPFA INLEVSKYSS SSLHVLFNVS CPVDSHTTKN FLIFAREQSD DSDYLHIAFN DLVFAEDKPV IESQWPKDAP ADEVSVVADK VSIQYRKWLR ELKEAHKEGS QAFRSALLDP VIESDRSYI |
-Experimental information
Beam | Instrument name: Photon Factory (PF), High Energy Accelerator Research Organization (KEK) BL-10C City: Tsukuba / 国: Japan / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.15 Å / Dist. spec. to detc.: 3 mm | ||||||||||||||||||
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Detector | Name: Pilatus3 2M / Pixsize x: 0.172 mm | ||||||||||||||||||
Scan | Title: Pseudomonas putida CBB5 NdmA hexamer / Measurement date: May 21, 2018 / Storage temperature: 4 °C / Cell temperature: 18 °C / Exposure time: 10 sec. / Number of frames: 32 / Unit: 1/A /
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Distance distribution function P(R) | Sofotware P(R): GNOM 5.0 / Number of points: 724 /
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Result | Experimental MW: 250 kDa / Type of curve: sec
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