8EJ0

Crystal structure of Fe-S cluster-dependent dehydratase from Paralcaligenes ureilyticus in complex with Mg


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

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Literature

Structural and Functional Insight into the Mechanism of the Fe-S Cluster-Dependent Dehydratase from Paralcaligenes ureilyticus.

Bayaraa, T.Lonhienne, T.Sutiono, S.Melse, O.Bruck, T.B.Marcellin, E.Bernhardt, P.V.Boden, M.Harmer, J.R.Sieber, V.Guddat, L.W.Schenk, G.

(2023) Chemistry 29: e202203140-e202203140

  • DOI: https://doi.org/10.1002/chem.202203140
  • Primary Citation of Related Structures:  
    8EJ0

  • PubMed Abstract: 

    Enzyme-catalyzed reaction cascades play an increasingly important role for the sustainable manufacture of diverse chemicals from renewable feedstocks. For instance, dehydratases from the ilvD/EDD superfamily have been embedded into a cascade to convert glucose via pyruvate to isobutanol, a platform chemical for the production of aviation fuels and other valuable materials. These dehydratases depend on the presence of both a Fe-S cluster and a divalent metal ion for their function. However, they also represent the rate-limiting step in the cascade. Here, catalytic parameters and the crystal structure of the dehydratase from Paralcaligenes ureilyticus (PuDHT, both in presence of Mg 2+ and Mn 2+ ) were investigated. Rate measurements demonstrate that the presence of stoichiometric concentrations Mn 2+ promotes higher activity than Mg 2+ , but at high concentrations the former inhibits the activity of PuDHT. Molecular dynamics simulations identify the position of a second binding site for the divalent metal ion. Only binding of Mn 2+ (not Mg 2+ ) to this site affects the ligand environment of the catalytically essential divalent metal binding site, thus providing insight into an inhibitory mechanism of Mn 2+ at higher concentrations. Furthermore, in silico docking identified residues that play a role in determining substrate binding and selectivity. The combined data inform engineering approaches to design an optimal dehydratase for the cascade.


  • Organizational Affiliation

    School of Chemistry and Molecular Biosciences, The University of Queensland, 4072, Brisbane, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroxyacid dehydrataseA,
B [auth C],
C [auth E],
D [auth G]
575Paralcaligenes ureilyticusMutation(s): 0 
Gene Names: EDC26_11947
UniProt
Find proteins for A0A4R3LQ44 (Paralcaligenes ureilyticus)
Explore A0A4R3LQ44 
Go to UniProtKB:  A0A4R3LQ44
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4R3LQ44
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
E [auth A],
I [auth C],
L [auth E],
Q [auth G]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth C]
N [auth E]
O [auth E]
G [auth A],
H [auth A],
K [auth C],
N [auth E],
O [auth E],
P [auth E]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CO2 (Subject of Investigation/LOI)
Query on CO2

Download Ideal Coordinates CCD File 
S [auth G]CARBON DIOXIDE
C O2
CURLTUGMZLYLDI-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth C],
M [auth E],
R [auth G]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
KCX
Query on KCX
A,
B [auth C],
C [auth E],
D [auth G]
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.908α = 90
b = 178.071β = 101.72
c = 92.858γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP210101802

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection
  • Version 1.2: 2024-09-11
    Changes: Database references