8VWR

Structure of steroid hydratase from Comamonas testosteroni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Shy is a proteobacterial steroid hydratase which catalyzes steroid side chain degradation without requiring a catalytically inert partner domain.

Schroeter, K.L.Rolfe, N.Forrester, T.J.B.Kimber, M.S.Seah, S.Y.K.

(2024) J Biol Chem 300: 107509-107509

  • DOI: https://doi.org/10.1016/j.jbc.2024.107509
  • Primary Citation of Related Structures:  
    8VWR

  • PubMed Abstract: 

    Shy (side chain hydratase) and Sal (side chain aldolase), are involved in successive reactions in the pathway of bile acid side chain catabolism in Proteobacteria. Untagged Shy co-purified with His-tagged Sal indicating that the two enzymes form a complex. Shy contains a MaoC and a DUF35 domain. When co-expressed with Sal, the DUF35 domain but not the MaoC domain of Shy was observed to co-purify with Sal, indicating Sal interacts with Shy through its DUF35 domain. The MaoC domain of Shy (Shy MaoC ) remained catalytically viable and could hydrate cholyl-enoyl-CoA with similar catalytic efficiency as in the Shy-Sal complex. Sal expressed with the DUF35 domain of Shy (Sal-Shy DUF35 ) was similarly competent for the retroaldol cleavage of cholyl-3-OH-CoA. Shy MaoC showed a preference for C 5 side chain bile acid substrates, exhibiting low activity towards C 3 side chain substrates. The Shy MaoC structure was determined by X-ray crystallography, showing a hot dog fold with a short central helix surrounded by a twisted anti-parallel β-sheet. Modeling and mutagenesis studies suggest that the bile acid substrate occupies the large open cleft formed by the truncated central helix and repositioning of the active site housing. Shy MaoC therefore contains two substrate binding sites per homodimer, making it distinct from previously characterized MaoC steroid hydratases that are (pseudo)-heterodimers with one substrate binding site per dimer. The characterization of Shy provides insight into how MaoC family hydratases have adapted to accommodate large polycyclic substrates that can facilitate future engineering of these enzymes to produce novel steroid pharmaceuticals.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Guelph, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl dehydratase
A, B
154Comamonas testosteroni KF-1Mutation(s): 0 
Gene Names: CtesDRAFT_PD3653
UniProt
Find proteins for B7X4S7 (Comamonas testosteroni (strain DSM 14576 / KF-1))
Explore B7X4S7 
Go to UniProtKB:  B7X4S7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7X4S7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
G [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
C [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B],
J [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.28α = 90
b = 95.28β = 90
c = 98.59γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada2020-04099
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada2020-07113

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references