Crystal structure of Escherichia coli Glycerol-3-phosphate Dehydrogenase in complex with 2-phospho-d-glyceric acid

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 

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Structure of glycerol-3-phosphate dehydrogenase, an essential monotopic membrane enzyme involved in respiration and metabolism

Yeh, J.I.Chinte, U.Du, S.

(2008) Proc Natl Acad Sci U S A 105: 3280-3285

  • DOI: https://doi.org/10.1073/pnas.0712331105
  • Primary Citation of Related Structures:  
    2QCU, 2R45, 2R46, 2R4E, 2R4J

  • PubMed Abstract: 

    Sn-glycerol-3-phosphate dehydrogenase (GlpD) is an essential membrane enzyme, functioning at the central junction of respiration, glycolysis, and phospholipid biosynthesis. Its critical role is indicated by the multitiered regulatory mechanisms that stringently controls its expression and function. Once expressed, GlpD activity is regulated through lipid-enzyme interactions in Escherichia coli. Here, we report seven previously undescribed structures of the fully active E. coli GlpD, up to 1.75 A resolution. In addition to elucidating the structure of the native enzyme, we have determined the structures of GlpD complexed with substrate analogues phosphoenolpyruvate, glyceric acid 2-phosphate, glyceraldehyde-3-phosphate, and product, dihydroxyacetone phosphate. These structural results reveal conformational states of the enzyme, delineating the residues involved in substrate binding and catalysis at the glycerol-3-phosphate site. Two probable mechanisms for catalyzing the dehydrogenation of glycerol-3-phosphate are envisioned, based on the conformational states of the complexes. To further correlate catalytic dehydrogenation to respiration, we have additionally determined the structures of GlpD bound with ubiquinone analogues menadione and 2-n-heptyl-4-hydroxyquinoline N-oxide, identifying a hydrophobic plateau that is likely the ubiquinone-binding site. These structures illuminate probable mechanisms of catalysis and suggest how GlpD shuttles electrons into the respiratory pathway. Glycerol metabolism has been implicated in insulin signaling and perturbations in glycerol uptake and catabolism are linked to obesity in humans. Homologs of GlpD are found in practically all organisms, from prokaryotes to humans, with >45% consensus protein sequences, signifying that these structural results on the prokaryotic enzyme may be readily applied to the eukaryotic GlpD enzymes.

  • Organizational Affiliation

    Departments of Structural Biology and Bioengineering, University of Pittsburgh School of Medicine, 3501 5th Avenue, BST3 1036, Pittsburgh, PA 15260, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aerobic glycerol-3-phosphate dehydrogenase
A, B
501Escherichia coliMutation(s): 0 
Gene Names: glpD
Find proteins for P13035 (Escherichia coli (strain K12))
Explore P13035 
Go to UniProtKB:  P13035
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13035
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

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DA [auth B],
L [auth A]
C27 H33 N9 O15 P2
Query on BOG

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C [auth A]
D [auth A]
E [auth A]
F [auth A]
X [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
X [auth B],
Y [auth B]
octyl beta-D-glucopyranoside
C14 H28 O6
Query on T3A

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MA [auth B],
U [auth A]
C7 H17 N O6 S
Query on 2PG

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OA [auth B],
W [auth A]
C3 H7 O7 P
Query on PO4

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AA [auth B]
BA [auth B]
CA [auth B]
G [auth A]
H [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
Z [auth B]
O4 P
Query on IMD

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LA [auth B],
M [auth A],
O [auth A]
C3 H5 N2
Query on EDO

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EA [auth B]
FA [auth B]
GA [auth B]
HA [auth B]
IA [auth B]
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
N [auth A],
NA [auth B],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
V [auth A]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.194 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.744α = 90
b = 113.908β = 90
c = 193.069γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Refinement description, Structure summary