9NXL | pdb_00009nxl

Crystal structure of steroid aldehyde dehydrogenase (Sad) from Caldimonas tepidiphilia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.192 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

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


This is version 1.0 of the entry. See complete history


Literature

Sad from Proteobacteria is a Structurally Distinct ALDH3 Enzyme Specialized for the Oxidation of Steroidal Aldehydes.

Rolfe, N.Myskiw, D.Patton, M.T.Forrester, T.J.B.Kimber, M.S.Seah, S.Y.K.

(2025) Biochemistry 64: 3735-3744

  • DOI: https://doi.org/10.1021/acs.biochem.5c00213
  • Primary Citation of Related Structures:  
    9NXL

  • PubMed Abstract: 

    The steroid aldehyde dehydrogenase (Sad) from Proteobacteria is a class 3 aldehyde dehydrogenase (ALDH3) that catalyzes the oxidation of C 3 steroid side chain aldehydes during bile acid catabolism. The 1.8 Å structure of the enzyme revealed an expanded active site that was able to accommodate bulky steroids, including bile acid intermediates and cholesterol derivatives, with minimal selectivity for ring-conformation or hydroxylation. Sad can utilize both NAD + and NADP + as coenzymes, likely due to a truncated N-terminus and a flexible Glu149 residue, which can avoid steric and electrostatic repulsion with the 2'-phosphate of NADP + while retaining the ability to hydrogen bond to the C2'-OH of NAD + . Sad was over 1000-fold more specific for steroid aldehyde substrates than for smaller molecules such as benzaldehyde. Structural comparison with the homologous Pseudomonas putida benzaldehyde dehydrogenase ( Pp BADH) suggested residues that might contribute to the ability of Sad to utilize bulky steroid substrates. Replacement of these residues in an F400A/L125T Pp BADH double-variant resulted in a ∼39-fold increase in catalytic efficiency toward steroid aldehyde compared with the wild-type enzyme. This study advances our understanding of the molecular determinants of substrate specificity within the ALDH3 family and lays the groundwork for biocatalytic applications of steroid aldehyde dehydrogenases in the production of steroid pharmaceuticals and the bioremediation of steroidal pollutants.


  • Organizational Affiliation
    • Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Steroid aldehyde dehydrogenase
A, B
476Caldimonas tepidiphilaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
H [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CAF
Query on CAF
A, B
L-PEPTIDE LINKINGC5 H12 As N O3 SCYS
CSO
Query on CSO
A, B
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.192 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.93α = 90
b = 89.45β = 90
c = 153.82γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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: 2025-10-08
    Type: Initial release