4UBW

Apo structure of the 3-ketoacyl-CoA thiolase FadA5 from M. tuberculosis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

FadA5 a Thiolase from Mycobacterium tuberculosis: A Steroid-Binding Pocket Reveals the Potential for Drug Development against Tuberculosis.

Schaefer, C.M., Lu, R., Nesbitt, N.M., Schiebel, J., Sampson, N.S., Kisker, C.

(2015) Structure 23: 21-33

  • DOI: 10.1016/j.str.2014.10.010
  • Primary Citation of Related Structures:  
    4UBT, 4UBU, 4UBV, 4UBW

  • PubMed Abstract: 

    • With the exception of HIV, tuberculosis (TB) is the leading cause of mortality among infectious diseases. The urgent need to develop new antitubercular drugs is apparent due to the increasing number of drug-resistant Mycobacterium tuberculosis (Mtb) strains ...

    With the exception of HIV, tuberculosis (TB) is the leading cause of mortality among infectious diseases. The urgent need to develop new antitubercular drugs is apparent due to the increasing number of drug-resistant Mycobacterium tuberculosis (Mtb) strains. Proteins involved in cholesterol import and metabolism have recently been discovered as potent targets against TB. FadA5, a thiolase from Mtb, is catalyzing the last step of the β-oxidation reaction of the cholesterol side-chain degradation under release of critical metabolites and was shown to be of importance during the chronic stage of TB infections. To gain structural and mechanistic insight on FadA5, we characterized the enzyme in different stages of the cleavage reaction and with a steroid bound to the binding pocket. Structural comparisons to human thiolases revealed that it should be possible to target FadA5 specifically, and the steroid-bound structure provides a solid basis for the development of inhibitors against FadA5.

    Organizational Affiliation: 

    Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany. Electronic address: caroline.kisker@virchow.uni-wuerzburg.de.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetyl-CoA acetyltransferase FadA5A, B399Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: fadA5, Rv3546, P425_03688, RVBD_3546, LH57_19345
EC: 2.3.1.16
UniProt
Find proteins for I6XHI4 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6XHI4 
Go to UniProtKB:  I6XHI4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6XHI4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A],
X [auth B],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
X [auth B],
Y [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
G [auth A],
GA [auth B],
H [auth A],
HA [auth B],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
Z [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
JA [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
IA [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.25α = 90
b = 128.25β = 90
c = 114.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB630
German Research FoundationGermanyFZ82
National Institutes of HealthUnited StatesAI092455
National Institutes of HealthUnited StatesAI085349
National Institutes of HealthUnited StatesAI065251
National Institutes of HealthUnited StatesHL53306
National Institutes of HealthUnited StatesRR021008
National Science Foundation (NSF, United States)United StatesBIO1039771

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 2.0: 2017-09-06
    Changes: Atomic model, Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 2.1: 2022-03-30
    Changes: Author supporting evidence, Database references