5TRR

Structure of Mycobacterium tuberculosis proteasome in complex with N,C-capped dipeptide PKS2169


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/10.1021/acs.biochem.6b01107
  • Primary Citation of Related Structures:  
    5THO, 5TRG, 5TRR, 5TRS, 5TRY, 5TS0

  • 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 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

    Van Andel Research Institute , Grand Rapids, Michigan 49503, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha
A, B, C, D, E
A, B, C, D, E, F, G, O, P, Q, R, S, T, U
240Mycobacterium tuberculosisMutation(s): 0 
Gene Names: prcAMRA_2124
EC: 3.4.25.1
UniProt
Find proteins for P9WHU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHU1 
Go to UniProtKB:  P9WHU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHU1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta240Mycobacterium tuberculosisMutation(s): 0 
Gene Names: prcBMRA_2125
EC: 3.4.25.1
UniProt
Find proteins for P9WHT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHT9 
Go to UniProtKB:  P9WHT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHT9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7HY
Query on 7HY

Download Ideal Coordinates CCD File 
CA [auth H]
DA [auth I]
EA [auth J]
FA [auth K]
GA [auth L]
CA [auth H],
DA [auth I],
EA [auth J],
FA [auth K],
GA [auth L],
HA [auth M],
IA [auth N],
JA [auth V],
KA [auth W],
LA [auth X],
MA [auth Y],
NA [auth Z],
OA [auth a],
PA [auth b]
N,N-diethyl-N~2~-(3-phenylpropanoyl)-L-asparaginyl-N-[(naphthalen-1-yl)methyl]-L-alaninamide
C31 H38 N4 O4
PVYXXOWWWHYLGR-CUNXSJBXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.297α = 90
b = 197.7β = 103.01
c = 165.184γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Data collection, Refinement description
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2020-08-12
    Changes: Structure summary
  • Version 1.6: 2023-10-04
    Changes: Data collection, Database references, Refinement description