4U0G | pdb_00004u0g

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

• PDB DOI: https://doi.org/10.2210/pdb4U0G/pdb

• Classification: hydrolase/antibiotic
• Organism(s): Mycobacterium tuberculosis H37Rv, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-07-11 Released: 2014-10-08 
• Deposition Author(s): Schmitz, K.R., Carney, D.W., Sello, J.K., Sauer, R.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.222 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

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

• PubMed: 25267638 
• DOI: https://doi.org/10.1073/pnas.1417120111
• Primary Citation Related Structures: 
  4U0G, 4U0H


• 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 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.

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Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and.
Department of Chemistry, Brown University, Providence, RI 02912.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Hetero 21-mer - A7B7C7 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 21-mer - A14B1C1D1E1F1G1H1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C7  (Explore in 3D)
Global Stoichiometry: Hetero 21-mer - A7B7C7 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 21-mer - A14B1C1D1E1F1G1H1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 638.29 kDa 
• Atom Count: 41,084 
• Modeled Residue Count: 5,264 
• Deposited Residue Count: 5,628 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 2	A, B, C, D, E, F, G, O, P, Q, R, S, T, U	202	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: clpP2, Rv2460c, MTV008.16c EC: 3.4.21.92
UniProt
Find proteins for P9WPC3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC3  Go to UniProtKB:  P9WPC3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 1	AA [auth a], BA [auth b], H, I, J, K, L, M, N, V, W, X, Y, Z	194	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: clpP1, clpP, Rv2461c, MTV008.17c EC: 3.4.21.92
UniProt
Find proteins for P9WPC5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC5  Go to UniProtKB:  P9WPC5

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ADEP-2B5Me	CA [auth c], DA [auth i], EA [auth d], FA [auth e], GA [auth f], HA [auth g], IA [auth h], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p]	6	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZIL	AC [auth M], BD [auth T], CC [auth N], DB [auth D], DC [auth O], ED [auth U], GB [auth E], HC [auth P], HD [auth V], ID [auth W], KD [auth X], LD [auth Y], MB [auth F], MC [auth Q], MD [auth Z], ND [auth a], OD [auth b], PB [auth G], QA [auth A], QC [auth R], TA [auth B], TB [auth H], UB [auth I], VC [auth S], WB [auth J], XA [auth C], YB [auth K], ZB [auth L]	N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine C20 H30 N2 O5 BSRAGXJNZJMFMY-XIRDDKMYSA-N
39Y	AE [auth n], BE [auth o], DE [auth p], PD [auth c], QD [auth i], RD [auth d], SD [auth e], TD [auth f], UD [auth g], VD [auth h], WD [auth j], XD [auth k], YD [auth l], ZD [auth m]	(2E,5S)-5-methylhept-2-enoic acid C8 H14 O2 WCNAROBWFNTKGN-KNIZRNDPSA-N
SO4	AB [auth C], BB [auth C], BC [auth M], CD [auth T], CE [auth p], EB [auth D], EC [auth O], FC [auth O], FD [auth U], HB [auth E], IB [auth E], IC [auth P], JB [auth E], JC [auth P], JD [auth W], KB [auth E], KC [auth P], NB [auth F], NC [auth Q], OC [auth Q], QB [auth G], RA [auth A], RB [auth G], RC [auth R], SC [auth R], TC [auth R], UA [auth B], VB [auth I], WC [auth S], XB [auth J], XC [auth S], YA [auth C], YC [auth S], ZA [auth C], ZC [auth S]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	AD [auth S], CB [auth C], DD [auth T], FB [auth D], GC [auth O], GD [auth U], LB [auth E], LC [auth P], OB [auth F], PC [auth Q], SA [auth A], SB [auth G], UC [auth R], VA [auth B], WA [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	AA [auth a], BA [auth b], H, I, J, K, L, M, N, V, W, X, Y, Z	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET
WFP	CA [auth c], DA [auth i], EA [auth d], FA [auth e], GA [auth f], HA [auth g], IA [auth h], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p]	L-PEPTIDE LINKING	C9 H9 F2 N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.222 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.748	α = 90
b = 187.673	β = 90
c = 294.029	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
Coot	model building
PDB_EXTRACT	data extraction
PHASER	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Schmitz, K.R., Carney, D.W., Sello, J.K., Sauer, R.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM-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
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
• Version 3.0: 2024-12-25
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary