4C6V

Crystal structure of M. tuberculosis KasA in complex with TLM5 (Soak for 5 min)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1074/jbc.M113.511436
  • Primary Citation of Related Structures:  

  • 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 ...

    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

    From the Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Wuerzburg, D-97080 Wuerzburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1
A
439N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
TLG
Query on TLG

Download SDF File 
Download CCD File 
A
(5R)-3-acetyl-4-hydroxy-5-methyl-5-[(1Z)-2-methylbuta-1,3-dien-1-yl]thiophen-2(5H)-one
C12 H14 O3 S
UBMUOEDBRIIXFH-ZHRWSRJISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TLGKd: 25600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.176 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.230α = 90.00
b = 77.230β = 90.00
c = 146.851γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-10-16
    Type: Database references
  • Version 1.2: 2013-10-23
    Type: Database references
  • Version 1.3: 2013-12-11
    Type: Database references