› 3ktj

X-ray diffraction
2.6Å resolution

Structure of ClpP in complex with ADEP2 in monoclinic crystal form

Released:
DOI: 10.2210/pdb3ktj/pdb
PDB entry 3ktj coloured by chain, front view.
PDB entry 3ktj coloured by chain, side view.
PDB entry 3ktj coloured by chain, top view.
Source organisms:
Primary publication:
Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism.
Lee BG, Park EY, Lee KE, Jeon H, Sung KH, Paulsen H, Rübsamen-Schaeff H, Brötz-Oesterhelt H, Song HK
Nat Struct Mol Biol 17 471-8 (2010)
PMID: 20305655

Function and Biology Details

Reaction catalysed: 
Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-Casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are hydrolyzed (such as succinyl-Leu-Tyr-|-NHMec; and Leu-Tyr-Leu-|-Tyr-Trp, in which cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp bonds also occurs).
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160376 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
ATP-dependent Clp protease proteolytic subunit Chains: A, B, C, D, E, F, G
Molecule details ›
Chains: A, B, C, D, E, F, G
Length: 199 amino acids
Theoretical weight: 21.99 KDa
Source organism: Bacillus subtilis
Expression system: Escherichia coli
UniProt:
  • Canonical: P80244 (Residues: 2-197; Coverage: 100%)
Gene names: BSU34540, clpP, yvdN
Sequence domains: Clp protease
Structure domains: 2-enoyl-CoA Hydratase; Chain A, domain 1
Acyldepsipeptide 2 Chains: H, I, J, K, L, M, N
Molecule details ›
Chains: H, I, J, K, L, M, N
Length: 7 amino acids
Theoretical weight: 817 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand NHE 7 x NHE
2 modified residues:
Ligand WFP 7 x WFP
Ligand MP8 7 x MP8

Experiments and Validation Details

Entry percentile scores
X-ray source: PAL/PLS BEAMLINE 4A
Spacegroup: C2
Unit cell:
a: 121.426Å b: 152.244Å c: 100.376Å
α: 90° β: 118.98° γ: 90°
R-values:
R R work R free
0.226 0.226 0.296
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

43 review citations

AAA+ proteases: ATP-fueled machines of protein destruction.
Sauer et al. (2011)
42 more

1 mention without citation

Structural insights into ClpP protease side exit pore-opening by a pH drop coupled with substrate hydrolysis.
Kim et al. (2022)