6CN8

High-resolution structure of ClpC1-NTD binding to Rufomycin-I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads.

Wolf, N.M.Lee, H.Choules, M.P.Pauli, G.F.Phansalkar, R.Anderson, J.R.Gao, W.Ren, J.Santarsiero, B.D.Lee, H.Cheng, J.Jin, Y.Y.Ho, N.A.Duc, N.M.Suh, J.W.Abad-Zapatero, C.Cho, S.

(2019) ACS Infect Dis 5: 829-840

  • DOI: 10.1021/acsinfecdis.8b00276
  • Primary Citation of Related Structures:  
    6CN8

  • PubMed Abstract: 
  • Addressing the urgent need to develop novel drugs against drug-resistant Mycobacterium tuberculosis ( M. tb) strains, ecumicin (ECU) and rufomycin I (RUFI) are being explored as promising new leads targeting cellular proteostasis via the caseinolytic protein ClpC1 ...

    Addressing the urgent need to develop novel drugs against drug-resistant Mycobacterium tuberculosis ( M. tb) strains, ecumicin (ECU) and rufomycin I (RUFI) are being explored as promising new leads targeting cellular proteostasis via the caseinolytic protein ClpC1. Details of the binding topology and chemical mode of (inter)action of these cyclopeptides help drive further development of novel potency-optimized entities as tuberculosis drugs. ClpC1 M. tb protein constructs with mutations driving resistance to ECU and RUFI show reduced binding affinity by surface plasmon resonance (SPR). Despite certain structural similarities, ECU and RUFI resistant mutation sites did not overlap in their SPR binding patterns. SPR competition experiments show ECU prevents RUFI binding, whereas RUFI partially inhibits ECU binding. The X-ray structure of the ClpC1-NTD-RUFI complex reveals distinct differences compared to the previously reported ClpC1-NTD-cyclomarin A structure. Surprisingly, the complex structure revealed that the epoxide moiety of RUFI opened and covalently bound to ClpC1-NTD via the sulfur atom of Met1. Furthermore, RUFI analogues indicate that the epoxy group of RUFI is critical for binding and bactericidal activity. The outcomes demonstrate the significance of ClpC1 as a novel target and the importance of SAR analysis of identified macrocyclic peptides for drug discovery.


    Organizational Affiliation

    Institute for Tuberculosis Research, College of Pharmacy , University of Illinois at Chicago , 833 S. Wood Street , Chicago , Illinois 60612 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP-dependent Clp protease ATP-binding subunit ClpC1A158Mycobacterium 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
Rufomycin IB7Streptomyces atratusMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MLE
Query on MLE
BL-PEPTIDE LINKINGC7 H15 N O2LEU
NIY
Query on NIY
BL-PEPTIDE LINKINGC9 H10 N2 O5TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002306
Query on PRD_002306
BRufomycin ICyclic peptide /  Antimicrobial Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.758α = 90
b = 109.758β = 90
c = 109.758γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Rural Development AdministrationKorea, Republic OfPJ01328403
Rural Development AdministrationKorea, Republic OfPJ01319101

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references