5L84

Structure of the H959F variant of the PpsC dehydratase domain from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Insights into Substrate Modification by Dehydratases from Type I Polyketide Synthases.

Faille, A.Gavalda, S.Slama, N.Lherbet, C.Maveyraud, L.Guillet, V.Laval, F.Quemard, A.Mourey, L.Pedelacq, J.D.

(2017) J Mol Biol 429: 1554-1569

  • DOI: 10.1016/j.jmb.2017.03.026
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Dehydration reactions play a crucial role in the de novo biosynthesis of fatty acids and a wide range of pharmacologically active polyketide natural products with strong emphasis on human medicine. The type I polyketide synthase PpsC from Mycobacteri ...

    Dehydration reactions play a crucial role in the de novo biosynthesis of fatty acids and a wide range of pharmacologically active polyketide natural products with strong emphasis on human medicine. The type I polyketide synthase PpsC from Mycobacterium tuberculosis catalyzes key biosynthetic steps of lipid virulence factors phthiocerol dimycocerosates and phenolic glycolipids. Given the insolubility of the natural C 28 -C 30 fatty acyl substrate of the PpsC dehydratase (DH) domain, we investigated its structure-function relationships in the presence of shorter surrogate substrates. Since most enzymes belonging to the (R)-specific enoyl hydratase/hydroxyacyl dehydratase family conduct the reverse hydration reaction in vitro, we have determined the X-ray structures of the PpsC DH domain, both unliganded (apo) and in complex with trans-but-2-enoyl-CoA or trans-dodec-2-enoyl-CoA derivatives. This study provides for the first time a snapshot of dehydratase-ligand interactions following a hydration reaction. Our structural analysis allowed us to identify residues essential for substrate binding and activity. The structural comparison of the two complexes also sheds light on the need for long acyl chains for this dehydratase to carry out its function, consistent with both its in vitro catalytic behavior and the physiological role of the PpsC enzyme.


    Organizational Affiliation

    Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31077 Toulouse Cedex 04, France. Electronic address: Jean-Denis.Pedelacq@ipbs.fr.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phthiocerol synthesis polyketide synthase type I PpsC
A
325Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: ppsCRv2933
EC: 2.3.1.41
Find proteins for P96202 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P96202
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.787α = 90
b = 83.787β = 90
c = 165.754γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance09-BLAN-0298-01

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection