1FGR

LIPOXYGENASE-1 (SOYBEAN) AT 100K, Q697E MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and functional characterization of second-coordination sphere mutants of soybean lipoxygenase-1.

Tomchick, D.R.Phan, P.Cymborowski, M.Minor, W.Holman, T.R.

(2001) Biochemistry 40: 7509-7517

  • DOI: 10.1021/bi002893d
  • Primary Citation of Related Structures:  
    1F8N, 1FGM, 1FGO, 1FGQ, 1FGR, 1FGT

  • PubMed Abstract: 
  • Lipoxygenases are an important class of non-heme iron enzymes that catalyze the hydroperoxidation of unsaturated fatty acids. The details of the enzymatic mechanism of lipoxygenases are still not well understood. This study utilizes a combination of kinetic and structural probes to relate the lipoxygenase mechanism of action with structural modifications of the iron's second coordination sphere ...

    Lipoxygenases are an important class of non-heme iron enzymes that catalyze the hydroperoxidation of unsaturated fatty acids. The details of the enzymatic mechanism of lipoxygenases are still not well understood. This study utilizes a combination of kinetic and structural probes to relate the lipoxygenase mechanism of action with structural modifications of the iron's second coordination sphere. The second coordination sphere consists of Gln(495) and Gln(697), which form a hydrogen bond network between the substrate cavity and the first coordination sphere (Asn(694)). In this investigation, we compared the kinetic and structural properties of four mutants (Q495E, Q495A, Q697N, and Q697E) with those of wild-type soybean lipoxygenase-1 and determined that changes in the second coordination sphere affected the enzymatic activity by hydrogen bond rearrangement and substrate positioning through interaction with Gln(495). The nature of the C-H bond cleavage event remained unchanged, which demonstrates that the mutations have not affected the mechanism of hydrogen atom tunneling. The unusual and dramatic inverse solvent isotope effect (SIE) observed for the Q697E mutant indicated that an Fe(III)-OH(-) is the active site base. A new transition state model for hydrogen atom abstraction is proposed.


    Related Citations: 
    • CRYSTAL STRUCTURE OF SOYBEAN LIPOXYGENASE L-1 AT 1.4 A RESOLUTION
      MINOR, W., STECZKO, J., STEC, B., OTWINOWSKI, Z., BOLIN, J.T., WALTER, R., AXELROD, B.
      (1996) Biochemistry 35: 10687
    • THE STRUCTURE AND FUNCTION OF LIPOXYGENASE
      NELSON, M.J., SEITZ, S.P.
      (1994) Curr Opin Struct Biol 4: 878
    • EXPERIMENTAL EVIDENCE FOR EXTENSIVE TUNNELING OF HYDROGEN IN THE LIPOXYGENASE REACTION: IMPLICATIONS FOR ENZYME CATALYSIS
      JONSSON, T., GLICKMAN, M.H., SUN, S., KLINMAN, J.P.
      (1996) J Am Chem Soc 118: 10319
    • NATURE OF THE RATE-LIMITING STEPS IN THE SOYBEAN LIPOXYGENASE-1 REACTION
      GLICKMAN, M.H., KLINMAN, J.P.
      (1995) Biochemistry 34: 14077
    • THE THREE-DIMENSIONAL STRUCTURE OF AN ARACHIDONIC ACID 15-LIPOXYGENASE
      BOYINGTON, J.C., GAFFNEY, B.J., AMZEL, L.M.
      (1993) Science 260: 1482
    • CRYSTALLOGRAPHIC DETERMINATION OF THE ACTIVE SITE IRON AND ITS LIGANDS IN SOYBEAN LIPOXYGENASE L-1
      MINOR, W., STECZKO, J., BOLIN, J.T., OTWINOWSKI, Z., AXELROD, B.
      (1993) Biochemistry 32: 6320
    • CRYSTALLIZATION AND PRELIMINARY X-RAY INVESTIGATION OF LIPOXYGENASE 1 FROM SOYBEANS
      STECZKO, J., MUCHMORE, C.R., L SMITH, J., AXELROD, B.
      (1990) J Biol Chem 265: 11352

    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SEED LIPOXYGENASE-1A839Glycine 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.42α = 90
b = 92.83β = 90.08
c = 49.36γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations