› 4u0g

X-ray diffraction
3.2Å resolution

Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP and agonist

Released:
DOI: 10.2210/pdb4u0g/pdb
PDB entry 4u0g coloured by chain, front view.
PDB entry 4u0g coloured by chain, side view.
PDB entry 4u0g coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery.
Schmitz KR, Carney DW, Sello JK, Sauer RT
Proc Natl Acad Sci U S A 111 E4587-95 (2014)
PMID: 25267638

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 21-mer (preferred)
PDBe Complex ID:
PDB-CPX-161943 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
ATP-dependent Clp protease proteolytic subunit 2 Chains: A, B, C, D, E, F, G, O, P, Q, R, S, T, U
Molecule details ›
Chains: A, B, C, D, E, F, G, O, P, Q, R, S, T, U
Length: 202 amino acids
Theoretical weight: 22.24 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WPC3 (Residues: 13-214; Coverage: 94%)
Gene names: MTV008.16c, Rv2460c, clpP2
Sequence domains: Clp protease
Structure domains: 2-enoyl-CoA Hydratase; Chain A, domain 1
ATP-dependent Clp protease proteolytic subunit 1 Chains: H, I, J, K, L, M, N, V, W, X, Y, Z, a, b
Molecule details ›
Chains: H, I, J, K, L, M, N, V, W, X, Y, Z, a, b
Length: 194 amino acids
Theoretical weight: 21.44 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WPC5 (Residues: 7-200; Coverage: 97%)
Gene names: MTV008.17c, Rv2461c, clpP, clpP1
Sequence domains: Clp protease
Structure domains: 2-enoyl-CoA Hydratase; Chain A, domain 1
ADEP-2B5Me Chains: c, d, e, f, g, h, i, j, k, l, m, n, o, p
Molecule details ›
Chains: c, d, e, f, g, h, i, j, k, l, m, n, o, p
Length: 7 amino acids
Theoretical weight: 817 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZIL 28 x ZIL
Ligand SO4 35 x SO4
Ligand DMS 15 x DMS
2 modified residues:
Ligand MSE 112 x MSE
Ligand WFP 14 x WFP

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 154.748Å b: 187.673Å c: 294.029Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.222
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

12 review citations

Mechanistic insights into bacterial AAA+ proteases and protein-remodelling machines.
Olivares et al. (2016)
11 more

11 mentions without citation

Recent structural insights into the mechanism of ClpP protease regulation by AAA+ chaperones and small molecules.
Mabanglo et al. (2022)
10 more