› 3w15

X-ray diffraction
1.8Å resolution

Structure of peroxisomal targeting signal 2 (PTS2) of Saccharomyces cerevisiae 3-ketoacyl-CoA thiolase in complex with Pex7p and Pex21p

Released:
DOI: 10.2210/pdb3w15/pdb
PDB entry 3w15 coloured by chain, front view.
PDB entry 3w15 coloured by chain, side view.
PDB entry 3w15 coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of peroxisomal targeting signal-2 bound to its receptor complex Pex7p-Pex21p.
Pan D, Nakatsu T, Kato H
Nat Struct Mol Biol 20 987-93 (2013)
PMID: 23812376

Function and Biology Details

Reaction catalysed: 
(1a) [acetyl-CoA C-acyltransferase]-S-acyl-L-cyteine + acetyl-CoA = 3-oxoacyl-CoA + [acetyl-CoA C-acyltransferase]-L-cyteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-142527 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Peroxisomal targeting signal 2 receptor Chain: A
Molecule details ›
Chain: A
Length: 368 amino acids
Theoretical weight: 41.53 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Komagataella pastoris
UniProt:
  • Canonical: P39108 (Residues: 1-375; Coverage: 98%)
Gene names: PAS7, PEB1, PEX7, YD2943.01C, YD9302.18C, YDR142C
Sequence domains: WD domain, G-beta repeat
Structure domains: YVTN repeat-like/Quinoprotein amine dehydrogenase
Peroxisomal protein PEX21 Chain: B
Molecule details ›
Chain: B
Length: 101 amino acids
Theoretical weight: 11 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P50091 (Residues: 190-288; Coverage: 34%)
Gene names: G8593, PEX21, YGR239C
Structure domains: Methane Monooxygenase Hydroxylase; Chain G, domain 1
3-ketoacyl-CoA thiolase, peroxisomal; Maltose/maltodextrin-binding periplasmic protein Chain: C
Molecule details ›
Chain: C
Length: 389 amino acids
Theoretical weight: 42.9 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: P27796 (Residues: 1-15; Coverage: 4%)
  • Canonical: P0AEX9 (Residues: 27-396; Coverage: 100%)
Gene names: FOX3, JW3994, POT1, POX3, YIL160C, b4034, malE
Sequence domains: Bacterial extracellular solute-binding protein
Structure domains: Periplasmic binding protein-like II

Ligands and Environments

2 bound ligands:
Ligand NO3 9 x NO3
Ligand MG 6 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 78.89Å b: 52.75Å c: 97.57Å
α: 90° β: 106.59° γ: 90°
R-values:
R R work R free
0.191 0.189 0.224
Expression systems:
  • Komagataella pastoris
  • Escherichia coli

Quick links

Citations

8 review citations

Current Advances in Protein Import into Peroxisomes.
Walter et al. (2019)
7 more

2 mentions without citation

The similarity between N-terminal targeting signals for protein import into different organelles and its evolutionary relevance.
Kunze et al. (2015)
1 more