7O4Q

Structure of Mycobacterium tuberculosis beta-oxidation trifunctional enzyme in space group C2221 (unliganded)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Substrate specificity and conformational flexibility properties of the Mycobacterium tuberculosis beta-oxidation trifunctional enzyme.

Dalwani, S.Lampela, O.Leprovost, P.Schmitz, W.Juffer, A.H.Wierenga, R.K.Venkatesan, R.

(2021) J Struct Biol 213: 107776-107776

  • DOI: https://doi.org/10.1016/j.jsb.2021.107776
  • Primary Citation of Related Structures:  
    7O1G, 7O1I, 7O1J, 7O1K, 7O1L, 7O1M, 7O4Q, 7O4R, 7O4S, 7O4T, 7O4U, 7O4V

  • PubMed Abstract: 

    The Mycobacterium tuberculosis trifunctional enzyme (MtTFE) is an α 2 β 2 tetrameric enzyme. The α-chain harbors the 2E-enoyl-CoA hydratase (ECH) and 3S-hydroxyacyl-CoA dehydrogenase (HAD) activities and the β-chain provides the 3-ketoacyl-CoA thiolase (KAT) activity. Enzyme kinetic data reported here show that medium and long chain enoyl-CoA molecules are preferred substrates for MtTFE. Modelling studies indicate how the linear medium and long acyl chains of these substrates can bind to each of the active sites. In addition, crystallographic binding studies have identified three new CoA binding sites which are different from the previously known CoA binding sites of the three TFE active sites. Structure comparisons provide new insights into the properties of ECH, HAD and KAT active sites of MtTFE. The interactions of the adenine moiety of CoA with loop-2 of the ECH active site cause a conformational change of this loop by which a competent ECH active site is formed. The NAD + binding domain (domain C) of the HAD part of MtTFE has only a few interactions with the rest of the complex and adopts a range of open conformations, whereas the A-domain of the ECH part is rigidly fixed with respect to the HAD part. Two loops, the CB1-CA1 region and the catalytic CB4-CB5 loop, near the thiolase active site and the thiolase dimer interface, have high B-factors. Structure comparisons suggest that a competent and stable thiolase dimer is formed only when complexed with the α-chains, highlighting the importance of the assembly for the proper functioning of the complex.


  • Organizational Affiliation

    Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-hydroxyacyl-CoA dehydrogenaseA [auth B]736Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: fadBRv0860
EC: 1.1.1.35
UniProt
Find proteins for O53872 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O53872 
Go to UniProtKB:  O53872
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO53872
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative acyltransferase Rv0859B [auth C]403Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: fadARv0859
EC: 2.3.1
UniProt
Find proteins for O53871 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O53871 
Go to UniProtKB:  O53871
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO53871
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
E [auth B]
F [auth B]
AA [auth C],
BA [auth C],
CA [auth C],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth B]
D [auth B]
P [auth C]
Q [auth C]
R [auth C]
C [auth B],
D [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.087α = 90
b = 204.685β = 90
c = 132.79γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland293369
Academy of FinlandFinland289024
Academy of FinlandFinland319194

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description