6D24

Trypanosoma cruzi Glucose-6-P Dehydrogenase in complex with G6P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Glucose-6-Phosphate Dehydrogenase from the Human Pathogen Trypanosoma cruzi Evolved Unique Structural Features to Support Efficient Product Formation.

Ortiz, C.Botti, H.Buschiazzo, A.Comini, M.A.

(2019) J Mol Biol 431: 2143-2162

  • DOI: 10.1016/j.jmb.2019.03.023
  • Primary Citation of Related Structures:  
    6D23, 6D24

  • PubMed Abstract: 
  • Glucose-6-phosphate dehydrogenase (G6PDH) is the key enzyme supplying reducing power (NADPH) to the cells, by oxidation of glucose-6-phosphate (G6P), and in the process providing a precursor of ribose-5-phosphate. G6PDH is also a virulence factor of pathogenic trypanosomatid parasites ...

    Glucose-6-phosphate dehydrogenase (G6PDH) is the key enzyme supplying reducing power (NADPH) to the cells, by oxidation of glucose-6-phosphate (G6P), and in the process providing a precursor of ribose-5-phosphate. G6PDH is also a virulence factor of pathogenic trypanosomatid parasites. To uncover the biochemical and structural features that distinguish TcG6PDH from its human homolog, we have solved and analyzed the crystal structures of the G6PDH from Trypanosoma cruzi (TcG6PDH), alone and in complex with G6P. TcG6PDH crystallized as a tetramer and enzymatic assays further indicated that the tetramer is the active form in the parasite, in contrast to human G6PDH, which displays higher activity as a dimer. This quaternary structure was shown to be particularly stable. The molecular reasons behind this disparity were unveiled by structural analyses: a TcG6PDH-specific residue, R323, is located at the dimer-dimer interface, critically contributing with two salt bridges per subunit that are absent in the human enzyme. This explains why TcG6PDH dimerization impaired enzyme activity. The parasite protein is also distinct in displaying a 37-amino-acid extension at the N-terminus, which comprises the non-conserved C8 and C34 involved in the covalent linkage of two neighboring protomers. In addition, a cysteine triad (C53, C94 and C135) specific of Kinetoplastid G6PDHs proved critical for stabilization of TcG6PDH active site. Based on the structural and biochemical data, we posit that the N-terminal region and the catalytic site are highly dynamic. The unique structural features of TcG6PDH pave the way toward the design of efficacious and highly specific anti-trypanosomal drugs.


    Related Citations: 
    • Expression, crystallization and preliminary X-ray crystallographic analysis of glucose-6-phosphate dehydrogenase from the human pathogen Trypanosoma cruzi in complex with substrate
      Ortiz, C., Larrieux, N., Medeiros, A., Botti, H., Comini, M., Buschiazzo, A.
      (2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 1457

    Organizational Affiliation

    Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay. Electronic address: mcomini@pasteur.edu.uy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-6-phosphate 1-dehydrogenaseA, B541Trypanosoma cruziMutation(s): 1 
Gene Names: G6PDH1C3747_142g63
EC: 1.1.1.49
UniProt
Find proteins for Q1WBU6 (Trypanosoma cruzi)
Explore Q1WBU6 
Go to UniProtKB:  Q1WBU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1WBU6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glucose-6-phosphate 1-dehydrogenaseC, D541Trypanosoma cruziMutation(s): 1 
Gene Names: G6PDH1C3747_142g63
EC: 1.1.1.49
UniProt
Find proteins for Q1WBU6 (Trypanosoma cruzi)
Explore Q1WBU6 
Go to UniProtKB:  Q1WBU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1WBU6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BG6
Query on BG6

Download Ideal Coordinates CCD File 
E [auth A],
EA [auth C],
R [auth B],
UA [auth D]
6-O-phosphono-beta-D-glucopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-VFUOTHLCSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
J [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
XA [auth D],
YA [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth D],
BB [auth D],
CB [auth D],
DA [auth C],
IA [auth C],
AB [auth D],
BB [auth D],
CB [auth D],
DA [auth C],
IA [auth C],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
P [auth A],
SA [auth C],
X [auth B],
ZA [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
DB [auth D],
EB [auth D],
AA [auth B],
BA [auth B],
CA [auth B],
DB [auth D],
EB [auth D],
FB [auth D],
GB [auth D],
HB [auth D],
IB [auth D],
JB [auth D],
M [auth A],
MA [auth C],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
PA [auth C],
Q [auth B],
QA [auth C],
RA [auth C],
TA [auth D],
Y [auth B],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
C, D L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.79α = 90
b = 133.03β = 100.27
c = 107.75γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
TRUNCATEdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-08-15
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.3: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary