6PBS

Structure of ClpC1-NTD in complex with Ecumicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.180 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions.

Wolf, N.M.Lee, H.Zagal, D.Nam, J.W.Oh, D.C.Lee, H.Suh, J.W.Pauli, G.F.Cho, S.Abad-Zapatero, C.

(2020) Acta Crystallogr D Struct Biol 76: 458-471

  • DOI: 10.1107/S2059798320004027
  • Primary Citation of Related Structures:  
    6UCR, 6PBA, 6PBQ, 6PBS

  • PubMed Abstract: 
  • The biological processes related to protein homeostasis in Mycobacterium tuberculosis, the etiologic agent of tuberculosis, have recently been established as critical pathways for therapeutic intervention. Proteins of particular interest are ClpC1 and the ClpC1-ClpP1-ClpP2 proteasome complex ...

    The biological processes related to protein homeostasis in Mycobacterium tuberculosis, the etiologic agent of tuberculosis, have recently been established as critical pathways for therapeutic intervention. Proteins of particular interest are ClpC1 and the ClpC1-ClpP1-ClpP2 proteasome complex. The structure of the potent antituberculosis macrocyclic depsipeptide ecumicin complexed with the N-terminal domain of ClpC1 (ClpC1-NTD) is presented here. Crystals of the ClpC1-NTD-ecumicin complex were monoclinic (unit-cell parameters a = 80.0, b = 130.0, c = 112.0 Å, β = 90.07°; space group P2 1 ; 12 complexes per asymmetric unit) and diffracted to 2.5 Å resolution. The structure was solved by molecular replacement using the self-rotation function to resolve space-group ambiguities. The new structure of the ecumicin complex showed a unique 1:2 (target:ligand) stoichiometry exploiting the intramolecular dyad in the α-helical fold of the target N-terminal domain. The structure of the ecumicin complex unveiled extensive interactions in the uniquely extended N-terminus, a critical binding site for the known cyclopeptide complexes. This structure, in comparison with the previously reported rufomycin I complex, revealed unique features that could be relevant for understanding the mechanism of action of these potential antituberculosis drug leads. Comparison of the ecumicin complex and the ClpC1-NTD-L92S/L96P double-mutant structure with the available structures of rufomycin I and cyclomarin A complexes revealed a range of conformational changes available to this small N-terminal helical domain and the minor helical alterations involved in the antibiotic-resistance mechanism. The different modes of binding and structural alterations could be related to distinct modes of action.


    Organizational Affiliation

    Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent Clp protease ATP-binding subunit ClpC1158Mycobacterium tuberculosisMutation(s): 0 
Gene Names: clpC1Rv3596cMTCY07H7B.26
UniProt
Find proteins for P9WPC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WPC9 
Go to UniProtKB:  P9WPC9
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ecumicin13Nonomuraea sp. MJM5123Mutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AB [auth K] , BB [auth M] , CB [auth O] , DB [auth T] , KA [auth A] , LA [auth A] , MA [auth I] , NA [auth I] , 
AB [auth K],  BB [auth M],  CB [auth O],  DB [auth T],  KA [auth A],  LA [auth A],  MA [auth I],  NA [auth I],  OA [auth C],  PA [auth W],  QA [auth W],  RA [auth W],  SA [auth W],  TA [auth Y],  UA [auth Y],  VA [auth Y],  WA [auth e],  XA [auth e],  YA [auth B],  ZA [auth G]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
H14
Query on H14
AA [auth Z] , BA [auth a] , CA [auth b] , DA [auth c] , EA [auth d] , FA [auth f] , GA [auth g] , HA [auth h] , 
AA [auth Z],  BA [auth a],  CA [auth b],  DA [auth c],  EA [auth d],  FA [auth f],  GA [auth g],  HA [auth h],  IA [auth i],  JA [auth j],  M [auth D],  N [auth E],  O [auth F],  P [auth H],  Q [auth J],  R [auth L],  S [auth N],  T [auth P],  U [auth Q],  V [auth R],  W [auth S],  X [auth U],  Y [auth V],  Z [auth X]
L-PEPTIDE LINKINGC9 H11 N O3PHE
MLE
Query on MLE
AA [auth Z] , BA [auth a] , CA [auth b] , DA [auth c] , EA [auth d] , FA [auth f] , GA [auth g] , HA [auth h] , 
AA [auth Z],  BA [auth a],  CA [auth b],  DA [auth c],  EA [auth d],  FA [auth f],  GA [auth g],  HA [auth h],  IA [auth i],  JA [auth j],  M [auth D],  N [auth E],  O [auth F],  P [auth H],  Q [auth J],  R [auth L],  S [auth N],  T [auth P],  U [auth Q],  V [auth R],  W [auth S],  X [auth U],  Y [auth V],  Z [auth X]
L-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
AA [auth Z] , BA [auth a] , CA [auth b] , DA [auth c] , EA [auth d] , FA [auth f] , GA [auth g] , HA [auth h] , 
AA [auth Z],  BA [auth a],  CA [auth b],  DA [auth c],  EA [auth d],  FA [auth f],  GA [auth g],  HA [auth h],  IA [auth i],  JA [auth j],  M [auth D],  N [auth E],  O [auth F],  P [auth H],  Q [auth J],  R [auth L],  S [auth N],  T [auth P],  U [auth Q],  V [auth R],  W [auth S],  X [auth U],  Y [auth V],  Z [auth X]
L-PEPTIDE LINKINGC6 H13 N O2VAL
NZC
Query on NZC
AA [auth Z] , BA [auth a] , CA [auth b] , DA [auth c] , EA [auth d] , FA [auth f] , GA [auth g] , HA [auth h] , 
AA [auth Z],  BA [auth a],  CA [auth b],  DA [auth c],  EA [auth d],  FA [auth f],  GA [auth g],  HA [auth h],  IA [auth i],  JA [auth j],  M [auth D],  N [auth E],  O [auth F],  P [auth H],  Q [auth J],  R [auth L],  S [auth N],  T [auth P],  U [auth Q],  V [auth R],  W [auth S],  X [auth U],  Y [auth V],  Z [auth X]
L-PEPTIDE LINKINGC5 H11 N O3THR
O7D
Query on O7D
AA [auth Z] , BA [auth a] , CA [auth b] , DA [auth c] , EA [auth d] , FA [auth f] , GA [auth g] , HA [auth h] , 
AA [auth Z],  BA [auth a],  CA [auth b],  DA [auth c],  EA [auth d],  FA [auth f],  GA [auth g],  HA [auth h],  IA [auth i],  JA [auth j],  M [auth D],  N [auth E],  O [auth F],  P [auth H],  Q [auth J],  R [auth L],  S [auth N],  T [auth P],  U [auth Q],  V [auth R],  W [auth S],  X [auth U],  Y [auth V],  Z [auth X]
L-PEPTIDE LINKINGC13 H16 N2 O3TRP
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002456
Query on PRD_002456
AA [auth D], BA [auth E], CA [auth F], DA [auth H], EA [auth J], FA [auth L], GA [auth N], HA [auth P], IA [auth Q], JA [auth R], M [auth S], N [auth U], O [auth V], P [auth X], Q [auth Z], R [auth a], S [auth b], T [auth c], U [auth d], V [auth f], W [auth g], X [auth h], Y [auth i], Z [auth j]ecumicinCyclic peptide /  Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.063α = 90
b = 130.342β = 90.07
c = 112.562γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 2.0: 2020-12-30
    Type: Coordinate replacement
    Reason: Chirality error
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Structure summary