› 1hr9

X-ray diffraction
3.01Å resolution

Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal Peptide

Released:
DOI: 10.2210/pdb1hr9/pdb
PDB entry 1hr9 coloured by chain, front view.
PDB entry 1hr9 coloured by chain, side view.
PDB entry 1hr9 coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences.
Taylor AB, Smith BS, Kitada S, Kojima K, Miyaura H, Otwinowski Z, Ito A, Deisenhofer J
Structure 9 615-25 (2001)
PMID: 11470436

Function and Biology Details

Reactions catalysed: 
Release of N-terminal targeting peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.
(S)-malate + NAD(+) = oxaloacetate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145325 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Mitochondrial-processing peptidase subunit alpha Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 475 amino acids
Theoretical weight: 52.53 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P11914 (Residues: 14-482; Coverage: 97%)
Gene names: MAS2, MIF2, YHR024C
Sequence domains:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
Mitochondrial-processing peptidase subunit beta Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 443 amino acids
Theoretical weight: 48.89 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P10507 (Residues: 21-462; Coverage: 96%)
Gene names: L9632.10, MAS1, MIF1, YLR163C
Sequence domains:
Structure domains: Metalloenzyme, LuxS/M16 peptidase-like
Malate dehydrogenase, mitochondrial Chains: O, P, Q, R
Molecule details ›
Chains: O, P, Q, R
Length: 8 amino acids
Theoretical weight: 903 Da
Source organism: Saccharomyces cerevisiae S288C
Expression system: Not provided
UniProt:
  • Canonical: P17505 (Residues: 2-9; Coverage: 2%)
Gene names: MDH1, YKL085W

Ligands and Environments

2 bound ligands:
Ligand ZN 4 x ZN
Ligand EPE 2 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P212121
Unit cell:
a: 134.37Å b: 178.52Å c: 201.95Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.217 0.256
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

37 review citations

Importing mitochondrial proteins: machineries and mechanisms.
Chacinska et al. (2009)
36 more

3 mentions without citation

Crystal and solution structures of a prokaryotic M16B peptidase: an open and shut case.
Aleshin et al. (2009)
2 more