Crystal structure of the hydroxyglutarate synthase from Pseudomonas putida

Experimental Data Snapshot

  • Resolution: 1.14 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism.

Thompson, M.G.Blake-Hedges, J.M.Pereira, J.H.Hangasky, J.A.Belcher, M.S.Moore, W.M.Barajas, J.F.Cruz-Morales, P.Washington, L.J.Haushalter, R.W.Eiben, C.B.Liu, Y.Skyrud, W.Benites, V.T.Barnum, T.P.Baidoo, E.E.K.Scheller, H.V.Marletta, M.A.Shih, P.M.Adams, P.D.Keasling, J.D.

(2020) Nat Commun 11: 2931-2931

  • DOI: https://doi.org/10.1038/s41467-020-16815-3
  • Primary Citation of Related Structures:  
    6W1G, 6W1H, 6W1K

  • PubMed Abstract: 

    Despite intensive study, plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remains unvalidated. Recently we described a missing step in the D-lysine catabolism of Pseudomonas putida in which 2OA is converted to D-2-hydroxyglutarate (2HG) via hydroxyglutarate synthase (HglS), a DUF1338 family protein. Here we solve the structure of HglS to 1.1 Å resolution in substrate-free form and in complex with 2OA. We propose a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O 2 -dependent manner. Specificity is mediated by a single arginine, highly conserved across most DUF1338 proteins. An Arabidopsis thaliana HglS homolog coexpresses with known lysine catabolism enzymes, and mutants show phenotypes consistent with disrupted lysine catabolism. Structural and biochemical analysis of Oryza sativa homolog FLO7 reveals identical activity to HglS despite low sequence identity. Our results suggest DUF1338-containing enzymes catalyze the same biochemical reaction, exerting the same physiological function across bacteria and eukaryotes.

  • Organizational Affiliation

    Joint BioEnergy Institute, Emeryville, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxyglutarate synthase464Pseudomonas putidaMutation(s): 0 
Gene Names: ydcJPP_5260
Find proteins for Q88CC1 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440))
Explore Q88CC1 
Go to UniProtKB:  Q88CC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ88CC1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NI (Subject of Investigation/LOI)
Query on NI

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.14 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.449α = 90
b = 100.746β = 90
c = 104.765γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description