4X28

Crystal structure of the ChsE4-ChsE5 complex from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Unraveling Cholesterol Catabolism in Mycobacterium tuberculosis: ChsE4-ChsE5 alpha 2 beta 2 Acyl-CoA Dehydrogenase Initiates beta-Oxidation of 3-Oxo-cholest-4-en-26-oyl CoA.

Yang, M.Lu, R.Guja, K.E.Wipperman, M.F.St Clair, J.R.Bonds, A.C.Garcia-Diaz, M.Sampson, N.S.

(2015) Acs Infect Dis. 1: 110-125

  • DOI: 10.1021/id500033m

  • PubMed Abstract: 
  • The metabolism of host cholesterol by Mycobacterium tuberculosis (Mtb) is an important factor for both its virulence and pathogenesis, although how and why cholesterol metabolism is required is not fully understood. Mtb uses a unique set of catabolic ...

    The metabolism of host cholesterol by Mycobacterium tuberculosis (Mtb) is an important factor for both its virulence and pathogenesis, although how and why cholesterol metabolism is required is not fully understood. Mtb uses a unique set of catabolic enzymes that are homologous to those required for classical β-oxidation of fatty acids but are specific for steroid-derived substrates. Here, we identify and assign the substrate specificities of two of these enzymes, ChsE4-ChsE5 (Rv3504-Rv3505) and ChsE3 (Rv3573c), that carry out cholesterol side chain oxidation in Mtb. Steady-state assays demonstrate that ChsE4-ChsE5 preferentially catalyzes the oxidation of 3-oxo-cholest-4-en-26-oyl CoA in the first cycle of cholesterol side chain β-oxidation that ultimately yields propionyl-CoA, whereas ChsE3 specifically catalyzes the oxidation of 3-oxo-chol-4-en-24-oyl CoA in the second cycle of β-oxidation that generates acetyl-CoA. However, ChsE4-ChsE5 can catalyze the oxidation of 3-oxo-chol-4-en-24-oyl CoA as well as 3-oxo-4-pregnene-20-carboxyl-CoA. The functional redundancy of ChsE4-ChsE5 explains the in vivo phenotype of the igr knockout strain of Mycobacterium tuberculosis; the loss of ChsE1-ChsE2 can be compensated for by ChsE4-ChsE5 during the chronic phase of infection. The X-ray crystallographic structure of ChsE4-ChsE5 was determined to a resolution of 2.0 Å and represents the first high-resolution structure of a heterotetrameric acyl-CoA dehydrogenase (ACAD). Unlike typical homotetrameric ACADs that bind four flavin adenine dinucleotide (FAD) cofactors, ChsE4-ChsE5 binds one FAD at each dimer interface, resulting in only two substrate-binding sites rather than the classical four active sites. A comparison of the ChsE4-ChsE5 substrate-binding site to those of known mammalian ACADs reveals an enlarged binding cavity that accommodates steroid substrates and highlights novel prospects for designing inhibitors against the committed β-oxidation step in the first cycle of cholesterol side chain degradation by Mtb.


    Organizational Affiliation

    Department of Chemistry, Department of Pharmacological Sciences, and Biochemistry and Structural Biology Graduate Program, Stony Brook University , Stony Brook, New York 11794, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acyl-CoA dehydrogenase
A, B
400Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: fadE26
EC: 1.3.99.-
Find proteins for I6YCA3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  I6YCA3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acyl-CoA dehydrogenase
D, C
373Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: fadE27
EC: 1.3.99.-
Find proteins for I6Y3Q0 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  I6Y3Q0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FDA
Query on FDA

Download SDF File 
Download CCD File 
A, B
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.151 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 185.745α = 90.00
b = 108.095β = 93.04
c = 82.019γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
XDSdata reduction
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM100021
National Institutes of Health/National Institute of Environmental Health SciencesUnited StatesF30-ES022930

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-07-22
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary