4U0G

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery.

Schmitz, K.R., Carney, D.W., Sello, J.K., Sauer, R.T.

(2014) Proc Natl Acad Sci U S A 111: E4587-E4595

  • DOI: 10.1073/pnas.1417120111
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Caseinolytic peptidase P (ClpP), a double-ring peptidase with 14 subunits, collaborates with ATPases associated with diverse activities (AAA+) partners to execute ATP-dependent protein degradation. Although many ClpP enzymes self-assemble into cataly ...

    Caseinolytic peptidase P (ClpP), a double-ring peptidase with 14 subunits, collaborates with ATPases associated with diverse activities (AAA+) partners to execute ATP-dependent protein degradation. Although many ClpP enzymes self-assemble into catalytically active homo-tetradecamers able to cleave small peptides, the Mycobacterium tuberculosis enzyme consists of discrete ClpP1 and ClpP2 heptamers that require a AAA+ partner and protein-substrate delivery or a peptide agonist to stabilize assembly of the active tetradecamer. Here, we show that cyclic acyldepsipeptides (ADEPs) and agonist peptides synergistically activate ClpP1P2 by mimicking AAA+ partners and substrates, respectively, and determine the structure of the activated complex. Our studies establish the basis of heteromeric ClpP1P2 assembly and function, reveal tight coupling between the conformations of each ring, show that ADEPs bind only to one ring but appear to open the axial pores of both rings, provide a foundation for rational drug development, and suggest strategies for studying the roles of individual ClpP1 and ClpP2 rings in Clp-family proteolysis.

    Organizational Affiliation: 

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and bobsauer@mit.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease proteolytic subunit 2A, B, C, D, E, F, G, O, P, Q, R, S, T, U202Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: clpP2, Rv2460c, MTV008.16c
EC: 3.4.21.92
Find proteins for P9WPC3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPC3 
Go to UniProtKB:  P9WPC3
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent Clp protease proteolytic subunit 1H, I, J, K, L, M, N, V, W, X, Y, Z, a, b194Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: clpP1, clpP, Rv2461c, MTV008.17c
EC: 3.4.21.92
Find proteins for P9WPC5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPC5 
Go to UniProtKB:  P9WPC5
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ADEP-2B5Mec, d, e, f, g, h, i, j, k, l, m, n, o, p7synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZIL
Query on ZIL
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b
N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine
C20 H30 N2 O5
BSRAGXJNZJMFMY-XIRDDKMYSA-N		 Ligand Interaction
SO4
Query on SO4
Download CCD File 
A, B, C, D, E, F, G, I, J, M, O, P, Q, R, S, T, U, W, p
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
DMS
Query on DMS
Download CCD File 
A, B, C, D, E, F, G, O, P, Q, R, S, T, U
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002111
Query on PRD_002111		c, d, e, f, g, h, i, j, k, l, m, n, o, pADEP-2B5MeC /  Antibiotic

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Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		H,I,J,K,L,M,N,V,W,X,Y,Z,a,bL-PEPTIDE LINKINGC5 H11 N O2 SeMET
WFP
Query on WFP		c,d,e,f,g,h,i,j,k,l,m,n,o,pL-PEPTIDE LINKINGC9 H9 F2 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.748α = 90
b = 187.673β = 90
c = 294.029γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
Cootmodel building
PDB_EXTRACTdata extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-101988

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-10-15
    Changes: Database references
  • Version 1.2: 2014-11-12
    Changes: Database references
  • Version 1.3: 2017-09-06
    Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence