6WY9

Tcur3481-Tcur3483 steroid ACAD G363A variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Key Glycine in Bacterial Steroid-Degrading Acyl-CoA Dehydrogenases Allows Flavin-Ring Repositioning and Modulates Substrate Side Chain Specificity.

Stirling, A.J.Gilbert, S.E.Conner, M.Mallette, E.Kimber, M.S.Seah, S.Y.K.

(2020) Biochemistry 59: 4081-4092

  • DOI: 10.1021/acs.biochem.0c00568
  • Primary Citation of Related Structures:  
    6WY9

  • PubMed Abstract: 
  • A wide variety of steroid metabolites synthesized by eukaryotes are all ultimately catabolized by bacteria; while generally saprophytic, pathogenic Mycobacteria have repurposed these pathways to utilize host intracellular cholesterol pools. Steroid d ...

    A wide variety of steroid metabolites synthesized by eukaryotes are all ultimately catabolized by bacteria; while generally saprophytic, pathogenic Mycobacteria have repurposed these pathways to utilize host intracellular cholesterol pools. Steroid degradation is complex, but a recurring theme is that cycles of β-oxidation are used to iteratively remove acetyl- or propanoyl-CoA groups. These β-oxidation cycles are initiated by the FAD-dependent oxidation of acyl groups, catalyzed by acyl-CoA dehydrogenases (ACADs). We show here that the tcur3481 and tcur3483 genes of Thermomonospora curvata encode subunits of a single ACAD that degrades steroid side chains with a preference for three-carbon over five-carbon substituents. The structure confirms that this enzyme is heterotetrameric, with active sites only in the Tcur3483 subunits. In comparison with the steroid ACAD FadE26-FadE27 from Mycobacterium tuberculosis , the active site is narrower and closed at the steroid-binding end, suggesting that Tcur3481-Tcur3483 is in a catalytically productive state, while FadE26-FadE27 is opened up to allow substrate entry. The flavin rings in Tcur3481-Tcur3483 sit in an unusual pocket created by Gly363, a residue conserved as Ala in steroid ACADs narrowly specific for five-carbon side chains, including FadE34. A Gly363Ala variant of Tcur3481-Tcur3483 prefers five-carbon side chains, while an inverse Ala691Gly FadE34 variant enables three-carbon side chain steroid oxidation. We determined the structure of the Tcur3483 Gly363Ala variant, showing that the flavin rings shift into the more conventional position. Modeling suggests that the shifted flavin position made possible by Gly363 is required to allow the bulky, inflexible three-carbon steroid to bind productively in the active site.


    Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 5E9.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl-CoA dehydrogenase domain protein Tcur3483A407Thermomonospora curvata DSM 43183Mutation(s): 1 
Gene Names: Tcur_3483
Find proteins for D1AB78 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9))
Explore D1AB78 
Go to UniProtKB:  D1AB78
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Acyl-CoA dehydrogenase domain protein Tcur3481B364Thermomonospora curvata DSM 43183Mutation(s): 0 
Gene Names: Tcur_3481
Find proteins for D1AB76 (Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9))
Explore D1AB76 
Go to UniProtKB:  D1AB76
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FDA
Query on FDA

Download CCD File 
A
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
 Ligand Interaction
1PE
Query on 1PE

Download CCD File 
A
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.5α = 90
b = 123.2β = 90
c = 139.21γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada04045-2015
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada2015-05366

Revision History 

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references