5OJG

Crystal structure of the dehydrogenase/reductase SDR family member 4 (DHRS4) from Caenorhabditis elegans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure and catalytic characterization of the dehydrogenase/reductase SDR family member 4 (DHRS4) from Caenorhabditis elegans.

Kisiela, M.Faust, A.Ebert, B.Maser, E.Scheidig, A.J.

(2018) FEBS J. 285: 275-293

  • DOI: 10.1111/febs.14337
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human dehydrogenase/reductase SDR family member 4 (DHRS4) is a tetrameric protein that is involved in the metabolism of several aromatic carbonyl compounds, steroids, and bile acids. The only invertebrate DHRS4 that has been characterized to date ...

    The human dehydrogenase/reductase SDR family member 4 (DHRS4) is a tetrameric protein that is involved in the metabolism of several aromatic carbonyl compounds, steroids, and bile acids. The only invertebrate DHRS4 that has been characterized to date is that from the model organism Caenorhabditis elegans. We have previously cloned and initially characterized this protein that was recently annotated as DHRS4_CAEEL in the UniProtKB database. Crystallization and X-ray diffraction studies of the full-length DHRS4_CAEEL protein in complex with diacetyl revealed its tetrameric structure and showed that two subunits are connected via an intermolecular disulfide bridge that is formed by N-terminal cysteine residues (Cys5) of each protein chain, which increases the enzymatic activity. A more detailed biochemical and catalytic characterization shows that DHRS4_CAEEL shares some properties with human DHRS4 such as relatively low substrate affinities with aliphatic α-diketones and a preference for aromatic dicarbonyls such as isatin, with a 30-fold lower Km value compared with the human enzyme. Moreover, DHRS4_CAEEL is active with aliphatic aldehydes (e.g. hexanal), while human DHRS4 is not. Dehydrogenase activity with alcohols was only observed with aromatic alcohols. Protein thermal shift assay revealed a stabilizing effect of phosphate buffer that was accompanied by an increase in catalytic activity of more than two-fold. The study of DHRS4 homologs in simple lineages such as C. elegans may contribute to our understanding of the original function of this protein that has been shaped by evolutionary processes in the course of the development from invertebrates to higher mammalian species.


    Organizational Affiliation

    Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School Schleswig-Holstein, Kiel, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dehydrogenase/reductase SDR family member 4
A, B
260Caenorhabditis elegansMutation(s): 0 
Gene Names: dhrs-4
EC: 1.1.1.184
Find proteins for G5EGA6 (Caenorhabditis elegans)
Go to UniProtKB:  G5EGA6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BUO
Query on BUO

Download SDF File 
Download CCD File 
A, B
butane-2,3-dione
C4 H6 O2
QSJXEFYPDANLFS-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 93.600α = 90.00
b = 93.600β = 90.00
c = 132.010γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyMA 1704/12-1

Revision History 

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy
  • Version 1.3: 2018-01-31
    Type: Database references