9MYR | pdb_00009myr

Sal-Shy(DUF35) aldolase from Comamonas testosteroni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.231 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Sal is a proteobacterial bile acid aldolase that repurposes key thiolase catalytic residues for retroaldol cleavage of C 5 steroid side chains.

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

(2025) J Biological Chem 301: 110439-110439

  • DOI: https://doi.org/10.1016/j.jbc.2025.110439
  • Primary Citation of Related Structures:  
    9MYR

  • PubMed Abstract: 

    Aldolases hold potential as biocatalysts for the synthesis of novel steroid pharmaceuticals. The steroid aldolase from Comamonas testosteroni (CtSal) forms a complex with C. testosteroni steroid hydratase (CtShy). CtSal cleaves the C 5 side chain of bile acid thioester steroids, whereas a previously characterized actinobacterial homolog from Thermonospora curvata (TcLtp2) targets the C 3 side chain. We identified Tyr302 and Cys304 as the catalytic residues in CtSal, different from the paired Tyr residues found in TcLtp2. The 1.95 Å structure of CtSal bound to the C-terminal domain of unknown function 35 (DUF35) of CtShy (CtShy DUF35 -CtSal) reveals a central CtSal dimer flanked by two CtShy DUF35 domains in an αββα arrangement. CtShy DUF35 has a unique Cys 3 His 1 (C 3 H 1 ) zinc finger that shapes the substrate-binding cleft of CtSal, preventing the binding of the flat cholesterol rings while accommodating the bent rings of bile acids. Phylogenetically, Sals and Ltp2s form separate clades and are distantly related to thiolases. Intriguingly, a Trypanosoma brucei homolog, annotated as a thiolase-like protein (TbSLP), shares the catalytic architecture of CtSal, suggesting an aldolase rather than a thiolase function. This study provides the first detailed characterization of a C 5 side chain steroid aldolase, revealing its unique catalytic features and expanding our understanding of steroid side chain catabolism in Proteobacteria.


  • Organizational Affiliation
    • Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nonspecific lipid-transfer protein
A, C
428Comamonas testosteroni KF-1Mutation(s): 0 
Gene Names: CtesDRAFT_PD3654
UniProt
Find proteins for B7X4S8 (Comamonas testosteroni (strain DSM 14576 / KF-1))
Explore B7X4S8 
Go to UniProtKB:  B7X4S8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7X4S8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl dehydratase
B, D
144Comamonas 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.231 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.46α = 90
b = 104.42β = 90
c = 112.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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: 2025-10-08
    Type: Initial release