3TZY

Crystal structure of a fragment containing the acyltransferase domain of Pks13 from Mycobacterium tuberculosis in the palmitoylated form at 2.2 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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Literature

Biochemical and structural study of the atypical acyltransferase domain from the mycobacterial polyketide synthase pks13

Bergeret, F.Gavalda, S.Chalut, C.Malaga, W.Quemard, A.Pedelacq, J.D.Daffe, M.Guilhot, C.Mourey, L.Bon, C.

(2012) J Biol Chem 287: 33675-33690

  • DOI: 10.1074/jbc.M111.325639
  • Primary Citation of Related Structures:  
    3TZW, 3TZX, 3TZY, 3TZZ

  • PubMed Abstract: 
  • Pks13 is a type I polyketide synthase involved in the final biosynthesis step of mycolic acids, virulence factors, and essential components of the Mycobacterium tuberculosis envelope. Here, we report the biochemical and structural characterization of a 52-kDa fragment containing the acyltransferase domain of Pks13 ...

    Pks13 is a type I polyketide synthase involved in the final biosynthesis step of mycolic acids, virulence factors, and essential components of the Mycobacterium tuberculosis envelope. Here, we report the biochemical and structural characterization of a 52-kDa fragment containing the acyltransferase domain of Pks13. This fragment retains the ability to load atypical extender units, unusually long chain acyl-CoA with a predilection for carboxylated substrates. High resolution crystal structures were determined for the apo, palmitoylated, and carboxypalmitoylated forms. Structural conservation with type I polyketide synthases and related fatty-acid synthases also extends to the interdomain connections. Subtle changes could be identified both in the active site and in the upstream and downstream linkers in line with the organization displayed by this singular polyketide synthase. More importantly, the crystallographic analysis illustrated for the first time how a long saturated chain can fit in the core structure of an acyltransferase domain through a dedicated channel. The structures also revealed the unexpected binding of a 12-mer peptide that might provide insight into domain-domain interaction.


    Organizational Affiliation

    Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, Toulouse, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyketide synthase PKS13A, B491Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv3800c
EC: 2.3.1
UniProt
Find proteins for O53579 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore O53579 
Go to UniProtKB:  O53579
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO53579
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
12-mer peptideC, D12Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.89α = 90
b = 105.89β = 90
c = 259.62γ = 90
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references