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› 4ka8

X-ray diffraction
1.9Å resolution

Structure of Organellar OligoPeptidase

Released:
DOI: 10.2210/pdb4ka8/pdb
Model geometry
Fit model/data
PDB entry 4ka8 coloured by chain, front view.
PDB entry 4ka8 coloured by chain, side view.
PDB entry 4ka8 coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts.
Kmiec B, Teixeira PF, Berntsson RP, Murcha MW, Branca RM, Radomiljac JD, Regberg J, Svensson LM, Bakali A, Langel U, Lehtiö J, Whelan J, Stenmark P, Glaser E
Proc Natl Acad Sci U S A 110 E3761-9 (2013)
PMID: 24043784

Function and Biology Details

Reaction catalysed: 
Hydrolysis of oligopeptides, with broad specificity. Gly or Ala commonlyoccur as P1 or P1' residues, but more distant residues are alsoimportant, as is shown by the fact that Z-Gly-Pro-Gly-|-Gly-Pro-Ala iscleaved, but not Z-(Gly)(5).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188215 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Organellar oligopeptidase A, chloroplastic/mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 714 amino acids
Theoretical weight: 80.27 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q94AM1 (Residues: 83-791; Coverage: 90%)
Gene names: At5g65620, K21L13.14, OOP, PRD1, TOP1
Sequence domains:
Structure domains: Neurolysin; domain 3

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand GOL 4 x GOL
Ligand NA 1 x NA
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P212121
Unit cell:
a: 71.817Å b: 101.339Å c: 132.908Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.191 0.218
Expression system: Escherichia coli

Quick links

Citations

9 review citations

Protein maturation and proteolysis in plant plastids, mitochondria, and peroxisomes.
van Wijk KJ. (2015)
8 more

1 mention without citation

Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts.
Kmiec et al. (2013)