Mycocerosic acid synthase exemplifies the architecture of reducing polyketide synthases

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Polyketide synthases (PKSs) are biosynthetic factories that produce natural products with important biological and pharmacological activities1,2,3. Their exceptional product diversity is encoded in a modular architecture. Modular PKSs (modPKSs) catalyse reactions colinear to the order of modules in an assembly line3, whereas iterative PKSs (iPKSs) use a single module iteratively as exemplified by fungal iPKSs (fiPKSs)3. However, in some cases non-colinear iterative action is also observed for modPKSs modules and is controlled by the assembly line environment4,5. PKSs feature a structural and functional separation into a condensing and a modifying region as observed for fatty acid synthases6. Despite the outstanding relevance of PKSs, the detailed organization of PKSs with complete fully reducing modifying regions remains elusive. Here we report a hybrid crystal structure of Mycobacterium smegmatis mycocerosic acid synthase based on structures of its condensing and modifying regions. Mycocerosic acid synthase is a fully reducing iPKS, closely related to modPKSs, and the prototype of mycobacterial mycocerosic acid synthase-like7,8 PKSs. It is involved in the biosynthesis of C20–C28 branched-chain fatty acids, which are important virulence factors of mycobacteria9. Our structural data reveal a dimeric linker-based organization of the modifying region and visualize dynamics and conformational coupling in PKSs. On the basis of comparative small-angle X-ray scattering, the observed modifying region architecture may be common also in modPKSs. The linker-based organization provides a rationale for the characteristic variability of PKS modules as a main contributor to product diversity. The comprehensive architectural model enables functional dissection and re-engineering of PKSs.

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Change history

  • Corrected online 23 March 2016

    Figure 4b was corrected to include a rotation axis line.


Data deposits

Atomic coordinates and structure factors for the reported crystal structures have been deposited in the Protein Data Bank under accession numbers 5BP1, 5BP2, 5BP3, 5BP4.


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Download references


We acknowledge F. Widdel and J. Zedelius for providing gammaproteobacterium HdN1, P. Leadlay and L. Betancor for providing plasmid pETcoco-2A-L1SL2, and EMBL Heidelberg for providing the pETG-10A vector; J. Missimer and A. Menzel for support in SAXS data acquisition and raw data processing; T. Sharpe for analytical ultracentrifugation, A. Mazur for SAXS refinement, and M. Bertoni for support of the homology-based assignment of the oligomeric state of MAS KS–AT. Data were collected at beamlines PXI, PXIII, and cSAXS of PSI; we acknowledge support from the beamline teams. This work was supported by the Swiss National Science Foundation project grants 125357, 138262, 159696 and R’equip grant 145023. D.A.H. acknowledges a fellowship by the Werner-Siemens Foundation.

Author information

Author notes

    • Dominik A. Herbst
    •  & Roman P. Jakob

    These authors contributed equally to this work.

    • Franziska Zähringer

    Present address: F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland.


  1. Department Biozentrum, University of Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland

    • Dominik A. Herbst
    • , Roman P. Jakob
    • , Franziska Zähringer
    •  & Timm Maier


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R.P.J. expressed, purified and crystallized MAS, obtained the crystal structure of the condensing region, collected SAXS data and cloned constructs. F.Z. cloned constructs and purified MAS, GpEryA and MsPks. D.A.H. purified MAS, optimized MAS crystallization, determined the structure of the isolated DH domains and the modifying region, collected SAXS data, analysed the data, performed homology modelling, cloned constructs, and wrote the manuscript. T.M. designed and guided research, analysed data, contributed to crystallographic analysis and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Timm Maier.

Extended data

Supplementary information


  1. 1.

    Conformational variability and coupling in the MAS modifying region

    All dimeric modifying regions of the MAS crystal structure were aligned to the DH domains and combined into one animation. The ER dimer moves in a screw motion with a lateral translation of up to 8.5Å and a rotation of up to 13.6° on the dimeric DH platform. The ER motion is linked to a rotation of the laterally double-tethered ΨKR/KR domains and couples the conformations of the ΨKR/KR across the MAS modifying region dimer. The maximum observed rotation of the ΨKR/KR domains (40.4°) causes an active site distance shift of 10 Å (euclidean space) relative to the DH domain.

  2. 2.

    Condensing region conformations in crystal structures of PKSs and FASs

    Structures of the homologous condensing regions are aligned and animated from MAS over PDB: 2QO3, 2HG4, 4MZ0, 2VZ9 to 3HHD. The superposition indicates a common hinge for rotational mapping of the AT domain positions located in the linker domain (grey). MAS adopts the most linear arrangement of all AT domains, which differs by a rotation of 43.2° around the common hinge from those observed in the crystal structure of human FAS (PDB: 3HHD).


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