1GYL

INVOLVEMENT OF TYR24 AND TRP108 IN SUBSTRATE BINDING AND SUBSTRATE SPECIFICITY OF GLYCOLATE OXIDASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 

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This is version 1.2 of the entry. See complete history


Literature

Involvement of Tyr24 and Trp108 in substrate binding and substrate specificity of glycolate oxidase.

Stenberg, K.Clausen, T.Lindqvist, Y.Macheroux, P.

(1995) Eur J Biochem 228: 408-416

  • Primary Citation of Related Structures:  
    1GYL

  • PubMed Abstract: 
  • Tyr24 and Trp108 are located in the active site of spinach glycolate oxidase. To elucidate their function in substrate binding and catalysis, they were replaced by phenylalanine and serine, respectively. The [Y24F]glycolate oxidase mutant enzyme showed a tenfold higher Km value for glycolate ...

    Tyr24 and Trp108 are located in the active site of spinach glycolate oxidase. To elucidate their function in substrate binding and catalysis, they were replaced by phenylalanine and serine, respectively. The [Y24F]glycolate oxidase mutant enzyme showed a tenfold higher Km value for glycolate. L-lactate and DL-2-hydroxybutyrate also showed higher Km values, however, the substrate specificity was unchanged as compared to the wild-type enzyme (Km increases in the order glycolate < DL-2-hydroxybutyrate < L-lactate < L-mandelate). The turnover number and the rate of reduction, found to be rate limiting in catalysis, were only slightly affected by the deletion of the hydroxyl group. These findings suggest that Tyr24 is mostly involved in substrate binding. The spectral features of the [Y24F]glycolate oxidase suggest that a fraction (50-80%) of the protein bears a flavin N(5) adduct instead of the oxidized cofactor. Crystals obtained from the isolated [Y24F]glycolate oxidase mutant protein allowed the determination of the three-dimensional structure. Although the structure was low resolution (0.3 nm), it is evident that the structure determined is that of the N(5) adduct species. In addition to the lacking hydroxyl group of Tyr24, we also observed movements of the amino acid side chains of Arg164 and Trp108, the latter replacing a water molecule in the substrate-binding pocket. Other features predominantly found in the class of flavoprotein oxidases, such as stabilization of the covalent N(5)-sulfite adduct and of the paraquinoid form of 8-mercapto-FMN, were found to be conserved. [W108S]Glycolate oxidase, in contrast, showed dramatic effects on both the Km of substrates as well as the turnover number. The Km for glycolate was increased some hundred fold and the turnover number was decreased 500-fold. In addition, it was found that the higher homologs of glycolate, L-lactate and DL-2-hydroxybutyrate had turnover numbers similar to those found with the wild-type enzyme, although the Km values also increased dramatically. These results indicate that Trp108 is of major importance in catalysis and that this residue is involved in determining the substrate specificity of glycolate oxidase.


    Related Citations: 
    • Role of Tyrosine 129 in the Active Site of Spinach Glycolate Oxidase
      Macheroux, P., Kieweg, V., Massey, V., Soderlind, E., Stenberg, K., Lindqvist, Y.
      (1993) Eur J Biochem 213: 1047
    • The Active Site of Spinach Glycolate Oxidase
      Lindqvist, Y., Branden, C.-I.
      (1989) J Biol Chem 264: 3624
    • Refined Structure of Spinach Glycolate Oxidase at 2 Angstroms Resolution
      Lindqvist, Y.
      (1989) J Mol Biol 209: 151

    Organizational Affiliation

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCOLATE OXIDASEA, B369Spinacia oleraceaMutation(s): 0 
Gene Names: GLYCOLATE OXIDASE FROM SPINACH
EC: 1.1.3.15
UniProt
Find proteins for P05414 (Spinacia oleracea)
Explore P05414 
Go to UniProtKB:  P05414
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05414
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.5α = 90
b = 145.5β = 90
c = 100.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-03-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance