6HL9

Crystal Structure of the CsiD Glutarate Hydroxylase in complex with Succinate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate.

Knorr, S.Sinn, M.Galetskiy, D.Williams, R.M.Wang, C.Muller, N.Mayans, O.Schleheck, D.Hartig, J.S.

(2018) Nat Commun 9: 5071-5071

  • DOI: 10.1038/s41467-018-07563-6
  • Primary Citation of Related Structures:  
    6HL9, 6HL8, 6GPN, 6GPE

  • PubMed Abstract: 
  • Lysine degradation has remained elusive in many organisms including Escherichia coli. Here we report catabolism of lysine to succinate in E. coli involving glutarate and L-2-hydroxyglutarate as intermediates. We show that CsiD acts as an α-ketoglutarate-dependent dioxygenase catalysing hydroxylation of glutarate to L-2-hydroxyglutarate ...

    Lysine degradation has remained elusive in many organisms including Escherichia coli. Here we report catabolism of lysine to succinate in E. coli involving glutarate and L-2-hydroxyglutarate as intermediates. We show that CsiD acts as an α-ketoglutarate-dependent dioxygenase catalysing hydroxylation of glutarate to L-2-hydroxyglutarate. CsiD is found widespread in bacteria. We present crystal structures of CsiD in complex with glutarate, succinate, and the inhibitor N-oxalyl-glycine, demonstrating strong discrimination between the structurally related ligands. We show that L-2-hydroxyglutarate is converted to α-ketoglutarate by LhgO acting as a membrane-bound, ubiquinone-linked dehydrogenase. Lysine enters the pathway via 5-aminovalerate by the promiscuous enzymes GabT and GabD. We demonstrate that repression of the pathway by CsiR is relieved upon glutarate binding. In conclusion, lysine degradation provides an important link in central metabolism. Our results imply the gut microbiome as a potential source of glutarate and L-2-hydroxyglutarate associated with human diseases such as cancer and organic acidurias.


    Organizational Affiliation

    Konstanz Research School Chemical Biology (KoRS-CB), Konstanz, 78457, Germany. joerg.hartig@uni-konstanz.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein CsiDA, B353Escherichia coli H386Mutation(s): 0 
Gene Names: csiDECVG_01093glaH
EC: 1.14.11.64
UniProt
Find proteins for A0A1X3JCQ2 (Escherichia coli H386)
Explore A0A1X3JCQ2 
Go to UniProtKB:  A0A1X3JCQ2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SIN
Query on SIN

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.034α = 90
b = 123.034β = 90
c = 138.327γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release