6EL3

Structure of Progesterone 5beta-Reductase from Arabidopsis thaliana in complex with NADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

PRISEs (progesterone 5 beta-reductase and/or iridoid synthase-like 1,4-enone reductases): Catalytic and substrate promiscuity allows for realization of multiple pathways in plant metabolism.

Schmidt, K.Petersen, J.Munkert, J.Egerer-Sieber, C.Hornig, M.Muller, Y.A.Kreis, W.

(2018) Phytochemistry 156: 9-19

  • DOI: https://doi.org/10.1016/j.phytochem.2018.08.012
  • Primary Citation of Related Structures:  
    6EL3

  • PubMed Abstract: 

    PRISEs (progesterone 5β-reductase and/or iridoid synthase-like 1,4-enone reductases) are involved in cardenolide and iridoid biosynthesis. We here investigated a PRISE (rAtSt5βR) from Arabidopsis thaliana, a plant producing neither cardenolides nor iridoids. The structure of rAtSt5βR was elucidated with X-ray crystallography and compared to the known structures of PRISEs from Catharanthus roseus (rCrISY) and Digitalis lanata (rDlP5βR). The three enzymes show a high degree of sequence and structure conservation in the active site. Amino acids previously considered to allow discrimination between progesterone 5β-reductase and iridoid synthase were interchanged among rAtSt5βR, rCrISY and rDlP5βR applying site-directed mutagenesis. Structural homologous substitutions had different effects, and changes in progesterone 5β-reductase and iridoid synthase activity were not correlated in all cases. Our results help to explain fortuitous emergence of metabolic pathways and product accumulation. The fact that PRISEs are found ubiquitously in spermatophytes insinuates that PRISEs might have a more general function in plant metabolism such as, for example, the detoxification of reactive carbonyl species.


  • Organizational Affiliation

    Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, D-91054 Erlangen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxo-Delta(4,5)-steroid 5-beta-reductase381Arabidopsis thalianaMutation(s): 0 
Gene Names: VEP1AWI31At4g24220T22A6.50
EC: 1.3.1.3
UniProt
Find proteins for Q9STX2 (Arabidopsis thaliana)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9STX2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxo-Delta(4,5)-steroid 5-beta-reductase381Arabidopsis thalianaMutation(s): 0 
Gene Names: VEP1AWI31At4g24220T22A6.50
EC: 1.3.1.3
UniProt
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9STX2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxo-Delta(4,5)-steroid 5-beta-reductase381Arabidopsis thalianaMutation(s): 0 
Gene Names: VEP1AWI31At4g24220T22A6.50
EC: 1.3.1.3
UniProt
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9STX2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxo-Delta(4,5)-steroid 5-beta-reductase381Arabidopsis thalianaMutation(s): 0 
Gene Names: VEP1AWI31At4g24220T22A6.50
EC: 1.3.1.3
UniProt
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UniProt GroupQ9STX2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxo-Delta(4,5)-steroid 5-beta-reductase381Arabidopsis thalianaMutation(s): 0 
Gene Names: VEP1AWI31At4g24220T22A6.50
EC: 1.3.1.3
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
3-oxo-Delta(4,5)-steroid 5-beta-reductase381Arabidopsis thalianaMutation(s): 0 
Gene Names: VEP1AWI31At4g24220T22A6.50
EC: 1.3.1.3
UniProt
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UniProt GroupQ9STX2
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.46α = 90
b = 94.86β = 90
c = 313.53γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description