› 6vxe

X-ray diffraction
2.46Å resolution

Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound

Released:
DOI: 10.2210/pdb6vxe/pdb
PDB 6vxe coloured by chain and viewed from the front.
PDB 6vxe coloured by chain and viewed from the side.
PDB 6vxe coloured by chain and viewed from the top.
Source organism: Clostridioides difficile 70-100-2010
Primary publication:
Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme.
Backman LR, Huang YY, Andorfer MC, Gold B, Raines RT, Balskus EP, Drennan CL
Elife 9 (2020)
PMID: 32180548

Function and Biology Details

Reaction catalysed: 
Trans-4-hydroxy-L-proline = (S)-1-pyrroline-5-carboxylate + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Trans-4-hydroxy-L-proline dehydratase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 809 amino acids
Theoretical weight: 91.46 KDa
Source organism: Clostridioides difficile 70-100-2010
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A031WDE4 (Residues: 1-789; Coverage: 100%)
Gene names: BGU81_07860, BN1095_640054, BN1096_740112, BN1097_360077, SAMEA3375004_02654, csdB_2, pflD
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand HYP 8 x HYP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 100.346Å b: 341.655Å c: 122.605Å
α: 90° β: 107.14° γ: 90°
R-values:
R R work R free
0.196 0.194 0.23
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase.
Dawson et al. (2021)
1 more