4FGW

Structure of Glycerol-3-Phosphate Dehydrogenase, GPD1, from Sacharomyces Cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of glycerol-3-phosphate dehydrogenase (GPD1) from Saccharomyces cerevisiae at 2.45A resolution

Alarcon, D.A.Nandi, M.Carpena, X.Fita, I.Loewen, P.C.

(2012) Acta Crystallogr.,Sect.F 68: 1279-1283

  • DOI: 10.1107/S1744309112037736

  • PubMed Abstract: 
  • The interconversion of glycerol 3-phosphate and dihydroxyacetone phosphate by glycerol-3-phosphate dehydrogenases provides a link between carbohydrate and lipid metabolism and provides Saccharomyces cerevisiae with protection against osmotic and anox ...

    The interconversion of glycerol 3-phosphate and dihydroxyacetone phosphate by glycerol-3-phosphate dehydrogenases provides a link between carbohydrate and lipid metabolism and provides Saccharomyces cerevisiae with protection against osmotic and anoxic stress. The first structure of a glycerol-3-phosphate dehydrogenase from S. cerevisiae, GPD1, is reported at 2.45 Å resolution. The asymmetric unit contains two monomers, each of which is organized with N- and C-terminal domains. The N-terminal domain contains a classic Rossmann fold with the (β-α-β-α-β)2 motif typical of many NAD+-dependent enzymes, while the C-terminal domain is mainly α-helical. Structural and phylogenetic comparisons reveal four main structure types among the five families of glycerol-3-phosphate and glycerol-1-phosphate dehydrogenases and reveal that the Clostridium acetobutylican protein with PDB code 3ce9 is a glycerol-1-phosphate dehydrogenase.


    Organizational Affiliation

    Institute for Research in Biomedicine, Parc Científic, Baldiri Reixac 10, 08028 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol-3-phosphate dehydrogenase [NAD(+)] 1
A, B
391Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: GPD1 (DAR1, HOR1, OSG1)
EC: 1.1.1.8
Find proteins for Q00055 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: GPD1
Go to UniProtKB:  Q00055
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.200 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 64.420α = 90.00
b = 64.420β = 90.00
c = 198.410γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
DNAdata collection
PHASERphasing
BUSTERrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references