5TRS

Structure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide PKS2144


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08357 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural Basis for the Species-Selective Binding of N,C-Capped Dipeptides to the Mycobacterium tuberculosis Proteasome.

Hsu, H.C.Singh, P.K.Fan, H.Wang, R.Sukenick, G.Nathan, C.Lin, G.Li, H.

(2017) Biochemistry 56: 324-333

  • DOI: 10.1021/acs.biochem.6b01107
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Mycobacterium tuberculosis (Mtb) 20S proteasome is vital for the pathogen to survive under nitrosative stress in vitro and to persist in mice. To qualify for drug development, inhibitors targeting Mtb 20S must spare both the human constitutive pr ...

    The Mycobacterium tuberculosis (Mtb) 20S proteasome is vital for the pathogen to survive under nitrosative stress in vitro and to persist in mice. To qualify for drug development, inhibitors targeting Mtb 20S must spare both the human constitutive proteasome (c-20S) and immunoproteasome (i-20S). We recently reported members of a family of noncovalently binding dipeptide proteasome inhibitors that are highly potent and selective for Mtb 20S over human c-20S and i-20S. To understand the structural basis of their potency and selectivity, we have studied the structure-activity relationship of six derivatives and solved their cocrystal structures with Mtb 20S. The dipeptide inhibitors form an antiparallel β-strand with the active site β-strands. Selectivity is conferred by several features of Mtb 20S relative to its mouse counterparts, including a larger S1 pocket, additional hydrogen bonds in the S3 pocket, and hydrophobic interactions in the S4 pocket. Serine-20 and glutamine-22 of Mtb 20S interact with the dipeptides and confer Mtb-specific inhibition over c-20S and i-20S. The Mtb 20S and mammalian i-20S have a serine-27 that interacts strongly with the dipeptides, potentially explaining the higher inhibitory activity of the dipeptides toward i-20S over c-20S. This detailed structural knowledge will aid in optimizing the dipeptides as anti-tuberculosis drugs.


    Organizational Affiliation

    NMR Analytical Core Facility, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States.,Van Andel Research Institute , Grand Rapids, Michigan 49503, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha
A, B, C, D, E, F, G, O, P, Q, R, S, T, U
240Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: prcA
EC: 3.4.25.1
Find proteins for P9WHU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHU1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta
H, I, J, K, L, M, N, V, W, X, Y, Z, a, b
240Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: prcB
EC: 3.4.25.1
Find proteins for P9WHT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHT9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7HZ
Query on 7HZ

Download SDF File 
Download CCD File 
a, b, H, I, J, K, L, M, N, V, W, X, Y, Z
N-tert-butoxy-N~2~-(5-methyl-1,2-oxazole-3-carbonyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamide
C28 H35 N5 O7
SDQPNMCIUPBBDV-GMAHTHKFSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002256 (7HZ)
Query on PRD_002256
a,b,H,I,J,K,L,M,N,V,W,X,Y,ZN-tert-butoxy-N~2~-(5-methyl-1,2-oxazole-3-carbonyl)-L-asparaginyl-O-methyl-N-[(naphthalen-1-yl)methyl]-L-serinamideNon-polymer / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.08357 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 120.509α = 90.00
b = 198.301β = 103.13
c = 165.941γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI070285

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-18
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection, Refinement description
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence
  • Version 1.4: 2019-12-11
    Type: Author supporting evidence