› 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 entry 6vxe coloured by chain, front view.
PDB entry 6vxe coloured by chain, side view.
PDB entry 6vxe coloured by chain, top view.
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:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-100140 (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

4 citation in other articles

Rescuing activity of oxygen-damaged pyruvate formate-lyase by a spare part protein.
Andorfer et al. (2021)
3 more

1 mention without citation

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