Crystal structure of M. tuberculosis C171Q KasA in complex with TLM5

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 

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This is version 1.4 of the entry. See complete history


Structural Basis for the Recognition of Mycolic Acid Precursors by Kasa, a Condensing Enzyme and Drug Target from Mycobacterium Tuberculosis

Schiebel, J.Kapilashrami, K.Fekete, A.Bommineni, G.R.Schaefer, C.M.Mueller, M.J.Tonge, P.J.Kisker, C.

(2013) J Biol Chem 288: 34190

  • DOI: https://doi.org/10.1074/jbc.M113.511436
  • Primary Citation of Related Structures:  
    4C6U, 4C6V, 4C6W, 4C6X, 4C6Z, 4C70, 4C71, 4C72, 4C73

  • PubMed Abstract: 

    The survival of Mycobacterium tuberculosis depends on mycolic acids, very long α-alkyl-β-hydroxy fatty acids comprising 60-90 carbon atoms. However, despite considerable efforts, little is known about how enzymes involved in mycolic acid biosynthesis recognize and bind their hydrophobic fatty acyl substrates. The condensing enzyme KasA is pivotal for the synthesis of very long (C38-42) fatty acids, the precursors of mycolic acids. To probe the mechanism of substrate and inhibitor recognition by KasA, we determined the structure of this protein in complex with a mycobacterial phospholipid and with several thiolactomycin derivatives that were designed as substrate analogs. Our structures provide consecutive snapshots along the reaction coordinate for the enzyme-catalyzed reaction and support an induced fit mechanism in which a wide cavity is established through the concerted opening of three gatekeeping residues and several α-helices. The stepwise characterization of the binding process provides mechanistic insights into the induced fit recognition in this system and serves as an excellent foundation for the development of high affinity KasA inhibitors.

  • Organizational Affiliation

    Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany; Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
439Mycobacterium tuberculosis H37RvMutation(s): 1 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on M7U

Download Ideal Coordinates CCD File 
P [auth A],
Z [auth B]
(2R)-2-(hexadecanoyloxy)-3-{[(10R)-10-methyloctadecanoyl]oxy}propyl phosphate
C38 H75 O8 P
Query on TLG

Download Ideal Coordinates CCD File 
O [auth A],
Y [auth B]
C12 H14 O3 S
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
C [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
C2 H6 O2
Query on K

Download Ideal Coordinates CCD File 
D [auth A],
Q [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
TLG PDBBind:  4C72 Ki: 8200 (nM) from 1 assay(s)
Binding MOAD:  4C72 Ki: 8200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.137 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.31α = 90
b = 89.1β = 90
c = 183.61γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-16
    Changes: Database references
  • Version 1.2: 2013-10-23
    Changes: Database references
  • Version 1.3: 2013-12-11
    Changes: Database references
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description