3T8W | pdb_00003t8w

A bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.200 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.164 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.166 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DGZClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases

Harbut, M.B.Velmourougane, G.Dalal, S.Reiss, G.Whisstock, J.C.Onder, O.Brisson, D.McGowan, S.Klemba, M.Greenbaum, D.C.

(2011) Proc Natl Acad Sci U S A 108: E526-E534

  • DOI: https://doi.org/10.1073/pnas.1105601108
  • Primary Citation of Related Structures:  
    3T8V, 3T8W

  • PubMed Abstract: 

    Malaria causes worldwide morbidity and mortality, and while chemotherapy remains an excellent means of malaria control, drug-resistant parasites necessitate the discovery of new antimalarials. Peptidases are a promising class of drug targets and perform several important roles during the Plasmodium falciparum erythrocytic life cycle. Herein, we report a multidisciplinary effort combining activity-based protein profiling, biochemical, and peptidomic approaches to functionally analyze two genetically essential P. falciparum metallo-aminopeptidases (MAPs), PfA-M1 and Pf-LAP. Through the synthesis of a suite of activity-based probes (ABPs) based on the general MAP inhibitor scaffold, bestatin, we generated specific ABPs for these two enzymes. Specific inhibition of PfA-M1 caused swelling of the parasite digestive vacuole and prevented proteolysis of hemoglobin (Hb)-derived oligopeptides, likely starving the parasite resulting in death. In contrast, inhibition of Pf-LAP was lethal to parasites early in the life cycle, prior to the onset of Hb degradation suggesting that Pf-LAP has an essential role outside of Hb digestion.


  • Organizational Affiliation

    Department of Pharmacology, University of Pennsylvania, 433 South University Avenue, 304G Lynch Laboratories, Philadelphia, PA 19104-6018, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
M17 leucyl aminopeptidase
A, B, C, D, E
528Plasmodium falciparum 3D7Mutation(s): 3 
EC: 3.4.13 (UniProt), 3.4.11.1 (UniProt)
UniProt
Find proteins for Q8IL11 (Plasmodium falciparum (isolate 3D7))
Explore Q8IL11 
Go to UniProtKB:  Q8IL11
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IL11
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGZ
Query on DGZ

Download Ideal Coordinates CCD File 
AC [auth H]
CA [auth C]
FD [auth K]
HB [auth F]
IC [auth I]
N-((2R,3S,6S,18S,21S)-2-amino-18-(4-benzoylbenzyl)-21-carbamoyl-3-hydroxy-6-(naphthalen-2-ylmethyl)-4,7,16,19-tetraoxo-1-phenyl-11,14-dioxa-5,8,17,20-tetraazapentacosan-25-yl)hex-5-ynamide
C57 H67 N7 O10
DTRONJOHRJXFLK-VGMISYGZSA-N
2PE
Query on 2PE

Download Ideal Coordinates CCD File 
EC [auth H],
Y [auth B]
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
AD [auth J]
BB [auth E]
BD [auth J]
CB [auth E]
DB [auth E]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth E]
BC [auth H]
CC [auth H]
DA [auth C]
DC [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
DD [auth K]
ED [auth K]
FB [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CO3
Query on CO3

Download Ideal Coordinates CCD File 
CD [auth K]
EB [auth F]
FC [auth I]
KA [auth D]
LB [auth G]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.200 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.164 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.166 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 173.748α = 90
b = 177.057β = 90
c = 231.221γ = 90
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted DGZClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations