6IUY

Structure of DsGPDH of Dunaliella salina


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The unusual di-domain structure of Dunaliella salina glycerol-3-phosphate dehydrogenase enables direct conversion of dihydroxyacetone phosphate to glycerol.

He, Q.Toh, J.D.Ero, R.Qiao, Z.Kumar, V.Serra, A.Tan, J.Sze, S.K.Gao, Y.G.

(2020) Plant J 102: 153-164

  • DOI: https://doi.org/10.1111/tpj.14619
  • Primary Citation of Related Structures:  
    6IUY

  • PubMed Abstract: 

    Dunaliella has been extensively studied due to its intriguing adaptation to high salinity. Its di-domain glycerol-3-phosphate dehydrogenase (GPDH) isoform is likely to underlie the rapid production of the osmoprotectant glycerol. Here, we report the structure of the chimeric Dunaliella salina GPDH (DsGPDH) protein featuring a phosphoserine phosphatase-like domain fused to the canonical glycerol-3-phosphate (G3P) dehydrogenase domain. Biochemical assays confirm that DsGPDH can convert dihydroxyacetone phosphate (DHAP) directly to glycerol, whereas a separate phosphatase protein is required for this conversion process in most organisms. The structure of DsGPDH in complex with its substrate DHAP and co-factor nicotinamide adenine dinucleotide (NAD) allows the identification of the residues that form the active sites. Furthermore, the structure reveals an intriguing homotetramer form that likely contributes to the rapid biosynthesis of glycerol.


  • Organizational Affiliation

    Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, College of Life Science and Technology, Southwest Minzu University, Chengdu, 610041, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol-3-phosphate dehydrogenase [NAD(+)]
A, B
624Dunaliella salinaMutation(s): 0 
EC: 1.1.1.8
UniProt
Find proteins for Q52ZA0 (Dunaliella salina)
Explore Q52ZA0 
Go to UniProtKB:  Q52ZA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ52ZA0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
13P (Subject of Investigation/LOI)
Query on 13P

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
1,3-DIHYDROXYACETONEPHOSPHATE
C3 H7 O6 P
GNGACRATGGDKBX-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.335α = 90
b = 91.335β = 90
c = 348.319γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (Singapore)SingaporeMOE2014-T2-1-083

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description