3WNV

Crystal structure of a glyoxylate reductase from Paecilomyes thermophila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Characterization and crystal structure of a first fungal glyoxylate reductase from Paecilomyes thermophila

Duan, X.Hu, S.Zhou, P.Zhou, Y.Liu, Y.Jiang, Z.

(2014) Enzyme.Microb.Technol. 60: 72-79

  • DOI: 10.1016/j.enzmictec.2014.04.004

  • PubMed Abstract: 
  • A glyoxylate reductase gene (PtGR) from the fungus Paecilomyces thermophila was cloned and expressed in Escherichia coli. PtGR was biochemically and structurally characterized. PtGR has an open reading frame of 993bp encoding 330 amino acids. The ded ...

    A glyoxylate reductase gene (PtGR) from the fungus Paecilomyces thermophila was cloned and expressed in Escherichia coli. PtGR was biochemically and structurally characterized. PtGR has an open reading frame of 993bp encoding 330 amino acids. The deduced amino acid sequence has low similarities to the reported glyoxylate reductases. The purified PtGR forms a homodimer. PtGR displayed an optimum pH of 7.5 and broad pH stability (pH 4.5-10). It exhibited an optimal temperature of 50°C and was stable up to 50°C. PtGR was found to be highly specific for glyoxylate, but it showed no detectable activity with 4-methyl-2-oxopentanoate, phenylglyoxylate, pyruvate, oxaloacetate and α-ketoglutarate. PtGR prefered NADPH rather than NADH as an electron donor. Moreover, the crystal structure of PtGR was determined at 1.75Å resolution. The overall structure of apo-PtGR monomer adopts the typical d-2-hydroxy-acid dehydrogenase fold with a "closed" conformation unexpectedly. The coenzyme specificity is provided by a cationic cluster consisting of N184, R185, and N186 structurally. These structural observations could explain its different coenzyme and substrate specificity.


    Organizational Affiliation

    Department of Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
glyoxylate reductase
A, B
330Paecilomyces sp. 'thermophila'Mutation(s): 0 
Find proteins for A0A0B4J185 (Paecilomyces sp. 'thermophila')
Go to UniProtKB:  A0A0B4J185
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.374α = 90.00
b = 62.763β = 94.28
c = 148.610γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release