6ICQ

Pseudomonas putida CBB5 NdmA QL mutant with theobromine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Mechanistic Insights into Caffeine Degradation by the Bacterial N-Demethylase Complex.

Kim, J.H.Kim, B.H.Brooks, S.Kang, S.Y.Summers, R.M.Song, H.K.

(2019) J.Mol.Biol. 431: 3647-3661

  • DOI: 10.1016/j.jmb.2019.08.004
  • Primary Citation of Related Structures:  

  • PubMed 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 soil. Some bacteria, such as Pseudomonas putida CB ...

    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 1 - and N 3 -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.


    Organizational Affiliation

    Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea. Electronic address: hksong@korea.ac.kr.,Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, AL 35487, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methylxanthine N1-demethylase NdmA
A, B, C
369Pseudomonas putidaMutation(s): 2 
Gene Names: ndmA
EC: 1.14.13.178
Find proteins for H9N289 (Pseudomonas putida)
Go to UniProtKB:  H9N289
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
37T
Query on 37T

Download SDF File 
Download CCD File 
A, B, C
THEOBROMINE
3,7-DIMETHYLXANTHINE, 3,7-DIMETHYLPURINE-2,6-DIONE
C7 H8 N4 O2
YAPQBXQYLJRXSA-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
A, B, C
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.946α = 90.00
b = 135.946β = 90.00
c = 155.637γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2016R1E1A1A01942623

Revision History 

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-09-25
    Type: Data collection, Database references