1X0X

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 
  • R-Value Observed: 0.182 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1016/j.jmb.2005.12.074
  • Primary Citation of Related Structures:  
    1WPQ, 1X0V, 1X0X

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic354Homo sapiensMutation(s): 0 
EC: 1.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P21695 (Homo sapiens)
Explore P21695 
Go to UniProtKB:  P21695
PHAROS:  P21695
GTEx:  ENSG00000167588 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21695
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.182 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.599α = 90
b = 116.599β = 90
c = 153.742γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations