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 

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:  
    1X0X, 1X0V, 1WPQ

  • 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmicA354Homo sapiensMutation(s): 0 
Gene Names: GPD1
EC: 1.1.1.8
Find proteins for P21695 (Homo sapiens)
Explore P21695 
Go to UniProtKB:  P21695
NIH Common Fund Data Resources
PHAROS:  P21695
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
G [auth A]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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 
  • 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

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2005-03-31 
  • 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