› 6el3

X-ray diffraction
1.9Å resolution

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

Released:
DOI: 10.2210/pdb6el3/pdb
PDB entry 6el3 coloured by chain, front view.
PDB entry 6el3 coloured by chain, side view.
PDB entry 6el3 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
PRISEs (progesterone 5β-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 YA, Kreis W
Phytochemistry 156 9-19 (2018)
PMID: 30172078

Function and Biology Details

Reaction catalysed: 
17,21-dihydroxy-5-beta-pregnane-3,11,20-trione + NADP(+) = cortisone + NADPH
Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193538 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
3-oxo-Delta(4,5)-steroid 5-beta-reductase Chain: A
Molecule details ›
Chain: A
Length: 381 amino acids
Theoretical weight: 44.06 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9STX2 (Residues: 17-388; Coverage: 96%)
Gene names: AWI31, At4g24220, T22A6.50, VEP1
Sequence domains: NAD dependent epimerase/dehydratase family
Structure domains: NAD(P)-binding Rossmann-like Domain
3-oxo-Delta(4,5)-steroid 5-beta-reductase Chain: B
Molecule details ›
Chain: B
Length: 381 amino acids
Theoretical weight: 44.08 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9STX2 (Residues: 17-388; Coverage: 96%)
Gene names: AWI31, At4g24220, T22A6.50, VEP1
Sequence domains: NAD dependent epimerase/dehydratase family
Structure domains: NAD(P)-binding Rossmann-like Domain
3-oxo-Delta(4,5)-steroid 5-beta-reductase Chain: C
Molecule details ›
Chain: C
Length: 381 amino acids
Theoretical weight: 44.06 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9STX2 (Residues: 17-388; Coverage: 96%)
Gene names: AWI31, At4g24220, T22A6.50, VEP1
Sequence domains: NAD dependent epimerase/dehydratase family
Structure domains: NAD(P)-binding Rossmann-like Domain
3-oxo-Delta(4,5)-steroid 5-beta-reductase Chain: D
Molecule details ›
Chain: D
Length: 381 amino acids
Theoretical weight: 44 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9STX2 (Residues: 17-388; Coverage: 96%)
Gene names: AWI31, At4g24220, T22A6.50, VEP1
Sequence domains: NAD dependent epimerase/dehydratase family
Structure domains: NAD(P)-binding Rossmann-like Domain
3-oxo-Delta(4,5)-steroid 5-beta-reductase Chain: E
Molecule details ›
Chain: E
Length: 381 amino acids
Theoretical weight: 44.06 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9STX2 (Residues: 17-388; Coverage: 96%)
Gene names: AWI31, At4g24220, T22A6.50, VEP1
Sequence domains: NAD dependent epimerase/dehydratase family
Structure domains: NAD(P)-binding Rossmann-like Domain
3-oxo-Delta(4,5)-steroid 5-beta-reductase Chain: F
Molecule details ›
Chain: F
Length: 381 amino acids
Theoretical weight: 43.97 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9STX2 (Residues: 17-388; Coverage: 96%)
Gene names: AWI31, At4g24220, T22A6.50, VEP1
Sequence domains: NAD dependent epimerase/dehydratase family
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAP 6 x NAP
1 bound ligand:
Ligand CL 6 x CL
1 modified residue:
Ligand MLY 74 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P212121
Unit cell:
a: 92.46Å b: 94.86Å c: 313.53Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.168 0.213
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Using interdisciplinary, phylogeny-guided approaches to understand the evolution of plant metabolism.
Schenck et al. (2022)
4 other articles

2 mentions without citation

Biosynthetic approach to combine the first steps of cardenolide formation in Saccharomyces cerevisiae.
Rieck et al. (2019)
1 more