6W1H

Crystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Pseudomonas putida


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

wwPDB Validation 3D Report Full Report



Literature

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: 10.1038/s41467-020-16815-3
  • Structures With Same Primary Citation

  • 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 ( ...

    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

    Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China. jdkeasling@lbl.gov.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydroxyglutarate synthase
A
464Pseudomonas putidaMutation(s): 0 
Gene Names: ydcJPP_5260
Find proteins for Q88CC1 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440))
Go to UniProtKB:  Q88CC1
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OOG
Query on OOG

Download CCD File 
A
2-OXOADIPIC ACID
C6 H8 O5
FGSBNBBHOZHUBO-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.442α = 90
b = 100.284β = 90
c = 103.577γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-06-24
    Type: Initial release