› 5mc2

X-ray diffraction
1.7Å resolution

Crystal Structure of Gly278Asp mutant of Human Prolidase with Mn ions and GlyPro ligand

Released:
DOI: 10.2210/pdb5mc2/pdb
PDB entry 5mc2 coloured by chain, front view.
PDB entry 5mc2 coloured by chain, side view.
PDB entry 5mc2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for prolidase deficiency disease mechanisms.
Wilk P, Uehlein M, Piwowarczyk R, Dobbek H, Mueller U, Weiss MS
FEBS J 285 3422-3441 (2018)
PMID: 30066404

Function and Biology Details

Reaction catalysed: 
Hydrolysis of Xaa-|-Pro dipeptides. Also acts on aminoacyl-hydroxyproline analogs. No action on Pro-|-Pro.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146399 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Xaa-Pro dipeptidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 484 amino acids
Theoretical weight: 53.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P12955 (Residues: 6-488; Coverage: 98%)
Gene names: PEPD, PRD
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand MN 2 x MN
Ligand NA 2 x NA
Ligand GLY 2 x GLY
Ligand PRO 2 x PRO
Ligand GOL 7 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: C2221
Unit cell:
a: 103.842Å b: 108.247Å c: 211.187Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.141 0.141 0.171
Expression system: Escherichia coli BL21

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Citations

4 review citations

Clinical Genetics of Prolidase Deficiency: An Updated Review.
Spodenkiewicz et al. (2020)
3 more

1 mention without citation

Structural basis for prolidase deficiency disease mechanisms.
Wilk et al. (2018)