5A0Z

STRUCTURE OF CUTC CHOLINE LYASE CHOLINE FREE FORM FROM KLEBSIELLA PNEUMONIAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and Function of Cutc Choline Lyase from Human Microbiota Bacterium Klebsiella Pneumoniaee

Kalnins, G.Kuka, J.Grinberga, S.Makrecka-Kuka, M.Liepinsh, E.Dambrova, M.Tars, K.

(2015) J Biol Chem 290: 21732

  • DOI: https://doi.org/10.1074/jbc.M115.670471
  • Primary Citation of Related Structures:  
    5A0U, 5A0Z

  • PubMed Abstract: 

    CutC choline trimethylamine-lyase is an anaerobic bacterial glycyl radical enzyme (GRE) that cleaves choline to produce trimethylamine (TMA) and acetaldehyde. In humans, TMA is produced exclusively by the intestinal microbiota, and its metabolite, trimethylamine oxide, has been associated with a higher risk of cardiovascular diseases. Therefore, information about the three-dimensional structures of TMA-producing enzymes is important for microbiota-targeted drug discovery. We have cloned, expressed, and purified the CutC GRE and the activating enzyme CutD from Klebsiella pneumoniae, a representative of the human microbiota. We have determined the first crystal structures of both the choline-bound and choline-free forms of CutC and have discovered that binding of choline at the ligand-binding site triggers conformational changes in the enzyme structure, a feature that has not been observed for any other characterized GRE.


  • Organizational Affiliation

    From the Latvian Biomedical Research and Study Center, LV-1067 Riga, gints@biomed.lu.lv.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CHOLINE TRIMETHYLAMINE LYASE
A, B, C, D
792Klebsiella pneumoniaeMutation(s): 0 
EC: 4.3.99.4
UniProt
Find proteins for A0A0M3KL45 (Klebsiella pneumoniae)
Explore A0A0M3KL45 
Go to UniProtKB:  A0A0M3KL45
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KL45
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.6α = 90
b = 154.55β = 96.85
c = 120.78γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references
  • Version 1.2: 2018-01-17
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Other, Refinement description