6W1K

Crystal structure of the hydroxyglutarate synthase in complex with 2-oxoadipate from Oryza sativa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxyglutarate synthase
A, B, C, D
322Oryza sativaMutation(s): 0 
Gene Names: OsJ_31810OSJNBa0071K18.7
UniProt
Find proteins for Q337M4 (Oryza sativa subsp. japonica)
Explore Q337M4 
Go to UniProtKB:  Q337M4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ337M4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OOG (Subject of Investigation/LOI)
Query on OOG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
S [auth C],
X [auth D]
2-OXOADIPIC ACID
C6 H8 O5
FGSBNBBHOZHUBO-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
G [auth A]
H [auth A]
K [auth B]
AA [auth D],
BA [auth D],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth C],
Q [auth C],
T [auth C],
U [auth C],
V [auth C],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
NI
Query on NI

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
R [auth C],
W [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.3α = 90
b = 98.2β = 90
c = 203.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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, Derived calculations, Refinement description