4B3I

Crystal structure of Mycobacterium tuberculosis fatty acid beta- oxidation complex with CoenzymeA bound at the hydratase active sites

• PDB DOI:  https://doi.org/10.2210/pdb4B3I/pdb

• Classification: OXIDOREDUCTASE/TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-07-24 Released: 2013-03-27 
• Deposition Author(s): Venkatesan, R., Wierenga, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.229 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Structure of Mycobacterial Beta-Oxidation Trifunctional Enzyme Reveals its Altered Assembly and Putative Substrate Channeling Pathway.

Venkatesan, R., Wierenga, R.K.

(2013) ACS Chem Biol 8: 1063

• PubMed: 23496842 
• DOI: https://doi.org/10.1021/cb400007k
• Primary Citation of Related Structures:  
  4B3H, 4B3I, 4B3J


• PubMed Abstract: 
  

The incidence of tuberculosis is increasing due to the appearance of new drug-resistant variants. A thorough understanding of the disease organism is essential in order to create more effective drugs. In an attempt to understand better the poorly studied lipid metabolism of Mycobacterium tuberculosis (Mtb), we identified and characterized its fatty acid β-oxidation complex (trifunctional enzyme (TFE)). TFE is an α(2)β(2) complex consisting of two types of polypeptides catalyzing three of the four reactions of the β-oxidation of fatty acids. The kinetic constants (k(cat) and K(m)) show that the complexed α chain is more active than the individual α chain. Crystal structures of Mtb TFE (mtTFE) reveal that the quaternary assembly is strikingly different from the already known Pseudomonas fragi TFE (pfTFE) assembly due to the presence of a helical insertion (LA5) in the mtTFE-β subunit. This helical insertion prevents the pfTFE mode of assembly, as it would clash with helix H9A of the TFE-α chain. The mtTFE assembly appears to be more rigid and results in a different substrate channeling path between the α and the β subunits. Structural comparisons suggest that the mtTFE active sites can accommodate bulkier fatty acyl chains than in pfTFE. Although another thiolase (FadA2), more closely related to human TFE-β/thiolase, is present in the Mtb genome, it does not form a complex with mtTFE-α. Extensive phylogenetic analyses show that there are at least four TFE subfamilies. Our studies highlight the molecular properties of mtTFE, significantly extending the structural knowledge on this type of very interesting multifunctional enzymes.

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Organizational Affiliation: 

Department of Biochemistry and Biocenter Oulu, University of Oulu, Oulu 90014, Finland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 246.67 kDa 
• Atom Count: 17,910 
• Modelled Residue Count: 2,264 
• Deposited Residue Count: 2,278 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FATTY ACID BETA-OXIDATION COMPLEX ALPHA-CHAIN FADB	A, B	736	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: fadB, Rv0860 EC: 4.2.1.17 (PDB Primary Data), 1.1.1.35 (PDB Primary Data)
UniProt
Find proteins for O53872 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53872  Go to UniProtKB:  O53872

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FATTY ACID BETA-OXIDATION COMPLEX BETA-CHAIN FADA	C, D	403	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: fadA, Rv0859 EC: 2.3.1.9 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for O53871 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53871  Go to UniProtKB:  O53871

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	N [auth A], Z [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
ADP	KA [auth C], O [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], LA [auth D], MA [auth D], NA [auth D], OA [auth D], P [auth B], PA [auth D], Q [auth B], QA [auth D], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	L [auth A], M [auth A], Y [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 0.229 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 248.16	α = 90
b = 135.97	β = 110.43
c = 118.16	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Venkatesan, R., Wierenga, R.K.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Database references