9B2G | pdb_00009b2g

Crystal structure of short chain dehydrogenase reductase 9 (short chain dehydrogenase reductase 9C4) in complex with NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.238 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

The effects of naturally occurring mutations on functionality of oxylipin metabolizing dehydrogenase reductase nine.

Wirth, S.E.Pakhomova, S.Belyaeva, O.V.Boeglin, W.E.Brash, A.R.Newcomer, M.E.Kedishvili, N.Y.Popov, K.M.

(2025) J Biological Chem 301: 110704-110704

  • DOI: https://doi.org/10.1016/j.jbc.2025.110704
  • Primary Citation of Related Structures:  
    9B2G

  • PubMed Abstract: 

    Recent evidence suggests that dehydrogenase reductase 9 (DHRS9) can oxidize and alter the biological activity of a diverse group of oxylipin substrates, underscoring the importance of DHRS9 in regulating various biological processes, including inflammation, cell proliferation, and tissue repair. Importantly, mutations in the DHRS9 gene resulting in amino acid substitutions S202L and D286H have been linked to an early-onset case of epilepsy; whether these mutations affect the function of DHRS9 has not been investigated. The results of this study demonstrate that both mutations cause a significant loss of DHRS9 functionality. However, in the case of the S202L variant, the loss of catalytic activity likely stems from the impaired protein folding and/or protein stability. On the other hand, the D286H DHRS9 mutant protein is relatively more stable than the S202L variant, but its K m value for NAD + (2.85 mM) is nearly 12-fold higher than that of the wild-type enzyme. The three-dimensional structure of DHRS9, solved in this study, provides insights into the functions of the S202 and D286 residues. In addition, it reveals a strikingly large substrate binding cavity, consistent with the fact that the enzyme can process oxygenated hydrocarbons with abundant rotational freedom and differing lengths (18-22 C). Considering that expression levels of DHRS9 in human tissues are highly sensitive to inflammatory conditions and the existence of naturally occurring mutations in DHRS9, the structural and functional characterization of DHRS9 reported in this study is critical for a better understanding of the role of DHRS9 in inflammatory processes.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehydrogenase/reductase SDR family member 9
A, B
319Mus musculusMutation(s): 0 
Gene Names: Dhrs9
EC: 1.1.1.209 (PDB Primary Data), 1.1.1.53 (PDB Primary Data), 1.1.1.105 (PDB Primary Data)
UniProt
Find proteins for Q58NB6 (Mus musculus)
Explore Q58NB6 
Go to UniProtKB:  Q58NB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58NB6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.238 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.116α = 90
b = 74.205β = 133.12
c = 102.771γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesAR076924
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM134548

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Database references