5TQN

Lipoxygenase-1 (soybean) L546A mutant at 293K

  • Classification: OXIDOREDUCTASE
  • Organism(s): Glycine max
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2016-10-24 Released: 2017-11-01 
  • Deposition Author(s): Poss, E.M., Fraser, J.S., Gee, C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Biophysical Characterization of a Disabled Double Mutant of Soybean Lipoxygenase: The "Undoing" of Precise Substrate Positioning Relative to Metal Cofactor and an Identified Dynamical Network.

Hu, S.Offenbacher, A.R.Thompson, E.M.Gee, C.L.Wilcoxen, J.Carr, C.A.M.Prigozhin, D.M.Yang, V.Alber, T.Britt, R.D.Fraser, J.S.Klinman, J.P.

(2019) J Am Chem Soc 141: 1555-1567

  • DOI: https://doi.org/10.1021/jacs.8b10992
  • Primary Citation of Related Structures:  
    5TQN, 5TQO, 5TR0

  • PubMed Abstract: 

    Soybean lipoxygenase (SLO) has served as a prototype for understanding the molecular origin of enzymatic rate accelerations. The double mutant (DM) L546A/L754A is considered a dramatic outlier, due to the unprecedented size and near temperature-independence of its primary kinetic isotope effect, low catalytic efficiency, and elevated enthalpy of activation. To uncover the physical basis of these features, we herein apply three structural probes: hydrogen-deuterium exchange mass spectrometry, room-temperature X-ray crystallography and EPR spectroscopy on four SLO variants (wild-type (WT) enzyme, DM, and the two parental single mutants, L546A and L754A). DM is found to incorporate features of each parent, with the perturbation at position 546 predominantly influencing thermally activated motions that connect the active site to a protein-solvent interface, while mutation at position 754 disrupts the ligand field and solvation near the cofactor iron. However, the expanded active site in DM leads to more active site water molecules and their associated hydrogen bond network, and the individual features from L546A and L754A alone cannot explain the aggregate kinetic properties for DM. Using recently published QM/MM-derived ground-state SLO-substrate complexes for WT and DM, together with the thorough structural analyses presented herein, we propose that the impairment of DM is the combined result of a repositioning of the reactive carbon of linoleic acid substrate with regard to both the iron cofactor and a catalytically linked dynamic region of protein.


  • Organizational Affiliation

    Department of Chemistry , East Carolina University , Greenville , North Carolina 27858 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Seed linoleate 13S-lipoxygenase-1
A, B
839Glycine maxMutation(s): 1 
Gene Names: LOX1.1LOX1
EC: 1.13.11.12
UniProt
Find proteins for P08170 (Glycine max)
Explore P08170 
Go to UniProtKB:  P08170
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08170
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.519α = 90
b = 92.656β = 93.47
c = 100.751γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM113432
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United States1S10RR022393-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM025765

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-01
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection
  • Version 1.2: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description