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Co-Structure of Homo Sapiens Glycerol-3-Phosphate Dehydrogenase 1 complex with NAD

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Crystal Structures of Human Glycerol 3-phosphate Dehydrogenase 1 (GPD1)

Ou, X., Ji, C., Han, X., Zhao, X., Li, X., Mao, Y., Wong, L.L., Bartlam, M., Rao, Z.

(2006) J.Mol.Biol. 357: 858-869

  • DOI: 10.1016/j.jmb.2005.12.074
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Homo sapiens L-alpha-glycerol-3-phosphate dehydrogenase 1 (GPD1) catalyzes the reversible biological conversion of dihydroxyacetone (DHAP) to glycerol-3-phosphate. The GPD1 protein was expressed in Escherichia coli, and purified as a fusion protein w ...

    Homo sapiens L-alpha-glycerol-3-phosphate dehydrogenase 1 (GPD1) catalyzes the reversible biological conversion of dihydroxyacetone (DHAP) to glycerol-3-phosphate. The GPD1 protein was expressed in Escherichia coli, and purified as a fusion protein with glutathione S-transferase. Here we report the apoenzyme structure of GPD1 determined by multiwavelength anomalous diffraction phasing, and other complex structures with small molecules (NAD+ and DHAP) by the molecular replacement method. This enzyme structure is organized into two distinct domains, the N-terminal eight-stranded beta-sheet sandwich domain and the C-terminal helical substrate-binding domain. An electrophilic catalytic mechanism by the epsilon-NH3+ group of Lys204 is proposed on the basis of the structural analyses. In addition, the inhibitory effects of zinc and sulfate on GPDHs are assayed and discussed.

    Organizational Affiliation: 

    National Laboratory of Biomacromolecules, Institute of Biophysics (IBP), Chinese Academy of Sciences, Beijing 100101, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic
A
354Homo sapiensMutation(s): 0 
Gene Names: GPD1
EC: 1.1.1.8
Find proteins for P21695 (Homo sapiens)
Go to Gene View: GPD1
Go to UniProtKB:  P21695
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAD
Query on NAD
Download SDF File 
Download CCD File 
A
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.178 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 116.599α = 90.00
b = 116.599β = 90.00
c = 153.742γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
MAR345data collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2005-03-31 
  • Released Date: 2006-04-11 
  • Deposition Author(s): Rao, Z., Ou, X.

Revision History 

  • Version 1.0: 2006-04-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description