1AL8

THREE-DIMENSIONAL STRUCTURE OF GLYCOLATE OXIDASE WITH BOUND ACTIVE-SITE INHIBITORS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structures of glycolate oxidase with bound active-site inhibitors.

Stenberg, K.Lindqvist, Y.

(1997) Protein Sci. 6: 1009-1015

  • DOI: 10.1002/pro.5560060506
  • Primary Citation of Related Structures:  1AL7

  • PubMed Abstract: 
  • A key step in plant photorespiration, the oxidation of glycolate to glyoxylate, is carried out by the peroxisomal flavoprotein glycolate oxidase (EC 1.1.3.15). The three-dimensional structure of this alpha/beta barrel protein has been refined to 2 A ...

    A key step in plant photorespiration, the oxidation of glycolate to glyoxylate, is carried out by the peroxisomal flavoprotein glycolate oxidase (EC 1.1.3.15). The three-dimensional structure of this alpha/beta barrel protein has been refined to 2 A resolution (Lindqvist Y. 1989. J Mol Biol 209:151-166). FMN dependent glycolate oxidase is a member of the family of alpha-hydroxy acid oxidases. Here we describe the crystallization and structure determination of two inhibitor complexes of the enzyme, TKP (3-Decyl-2,5-dioxo-4-hydroxy-3-pyrroline) and TACA (4-Carboxy-5-(1-pentyl)hexylsulfanyl-1,2,3-triazole). The structure of the TACA complex has been refined to 2.6 A resolution and the TKP complex, solved with molecular replacement, to 2.2 A resolution. The Rfree for the TACA and TKP complexes are 24.2 and 25.1%, respectively. The overall structures are very similar to the unliganded holoenzyme, but a closer examination of the active site reveals differences in the positioning of the flavin isoalloxazine ring and a displaced flexible loop in the TKP complex. The two inhibitors differ in binding mode and hydrophobic interactions, and these differences are reflected by the very different Ki values for the inhibitors, 16 nM for TACA and 4.8 microM for TKP. Implications of the structures of these enzyme-inhibitor complexes for the model for substrate binding and catalysis proposed from the holo-enzyme structure are discussed.


    Related Citations: 
    • High-Level Expression, Purification and Crystallization of Recombinant Spinach Glycolate Oxidase in Escherichia Coli
      Stenberg, K.,Lindqvist, Y.
      (1996) Protein Expr.Purif. 8: 295
    • Refined Structure of Spinach Glycolate Oxidase at 2 A Resolution
      Lindqvist, Y.
      (1989) J.Mol.Biol. 209: 151


    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska, Institute, Stockholm, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOLATE OXIDASE
A
359Spinacia oleraceaEC: 1.1.3.15
Find proteins for P05414 (Spinacia oleracea)
Go to UniProtKB:  P05414
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
DHP
Query on DHP

Download SDF File 
Download CCD File 
A
3-DECYL-2,5-DIOXO-4-HYDROXY-3-PYRROLINE
C14 H23 N O3
LXIDJQZEXUQBGG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DHPKi: 4800 nM BINDINGMOAD
DHPKi: 4800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.194 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 95.400α = 90.00
b = 95.400β = 90.00
c = 93.500γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-09-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance