Crystal structure of HsaD from Mycobacterium tuberculosis in complex with Cyclipostin-like inhibitor CyC31

Experimental Data Snapshot

  • Resolution: 1.62 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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Direct capture, inhibition and crystal structure of HsaD (Rv3569c) from M. tuberculosis.

Barelier, S.Avellan, R.Gnawali, G.R.Fourquet, P.Roig-Zamboni, V.Poncin, I.Point, V.Bourne, Y.Audebert, S.Camoin, L.Spilling, C.D.Canaan, S.Cavalier, J.F.Sulzenbacher, G.

(2023) FEBS J 290: 1563-1582

  • DOI: https://doi.org/10.1111/febs.16645
  • Primary Citation of Related Structures:  
    7ZJT, 7ZM1, 7ZM2, 7ZM3, 7ZM4

  • PubMed Abstract: 

    A hallmark of Mycobacterium tuberculosis (M. tb), the aetiologic agent of tuberculosis, is its ability to metabolise host-derived lipids. However, the enzymes and mechanisms underlying such metabolism are still largely unknown. We previously reported that the Cyclophostin & Cyclipostins (CyC) analogues, a new family of potent antimycobacterial molecules, react specifically and covalently with (Ser/Cys)-based enzymes mostly involved in bacterial lipid metabolism. Here, we report the synthesis of new CyC alkyne-containing inhibitors (CyC yne ) and their use for the direct fishing of target proteins in M. tb culture via bio-orthogonal click-chemistry activity-based protein profiling (CC-ABPP). This approach led to the capture and identification of a variety of enzymes, and many of them involved in lipid or steroid metabolisms. One of the captured enzymes, HsaD (Rv3569c), is required for the survival of M. tb within macrophages and is thus a potential therapeutic target. This prompted us to further explore and validate, through a combination of biochemical and structural approaches, the specificity of HsaD inhibition by the CyC analogues. We confirmed that the CyC bind covalently to the catalytic Ser 114 residue, leading to a total loss of enzyme activity. These data were supported by the X-ray structures of four HsaD-CyC complexes, obtained at resolutions between 1.6 and 2.6 Å. The identification of mycobacterial enzymes directly captured by the CyC yne probes through CC-ABPP paves the way to better understand and potentially target key players at crucial stages of the bacilli life cycle.

  • Organizational Affiliation

    CNRS, AFMB, Aix-Marseille University, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
A, B
299Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: hsaDbphDRv3569c
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for P9WNH5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNH5 
Go to UniProtKB:  P9WNH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNH5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.62 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.684α = 90
b = 87.224β = 90
c = 105.725γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)France--

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-28
    Type: Initial release
  • Version 1.1: 2022-10-19
    Changes: Database references
  • Version 1.2: 2023-03-29
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description