4IEC

Cys105 covalent modification by 2-hydroxyethyl disulfide in Mycobacterium tuberculosis methionine aminopeptidase Type 1c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selective targeting of the conserved active site cysteine of Mycobacterium tuberculosis methionine aminopeptidase with electrophilic reagents

Reddi, R.Arya, T.Kishor, C.Gumpena, R.Ganji, R.J.Bhukya, S.Addlagatta, A.

(2014) Febs J. 281: 4240-4248

  • DOI: 10.1111/febs.12847
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Methionine aminopeptidases (MetAPs) cleave initiator methionine from ~ 70% of the newly synthesized proteins in every living cell, and specific inhibition or knockdown of this function is detrimental. MetAPs are metalloenzymes, and are broadly classi ...

    Methionine aminopeptidases (MetAPs) cleave initiator methionine from ~ 70% of the newly synthesized proteins in every living cell, and specific inhibition or knockdown of this function is detrimental. MetAPs are metalloenzymes, and are broadly classified into two subtypes, type I and type II. Bacteria contain only type I MetAPs, and the active site of these enzymes contains a conserved cysteine. By contrast, in type II enzymes the analogous position is occupied by a conserved glycine. Here, we report the reactivity of the active site cysteine in a type I MetAP, MetAP1c, of Mycobacterium tuberculosis (MtMetAP1c) towards highly selective cysteine-specific reagents. The authenticity of selective modification of Cys105 of MtMetAP1c was established by using site-directed mutagenesis and crystal structure determination of covalent and noncovalent complexes. On the basis of these observations, we propose that metal ions in the active site assist in the covalent modification of Cys105 by orienting the reagents appropriately for a successful reaction. These studies establish, for the first time, that the conserved cysteine of type I MetAPs can be targeted for selective inhibition, and we believe that this chemistry can be exploited for further drug discovery efforts regarding microbial MetAPs.


    Organizational Affiliation

    Center for Chemical Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telengana, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionine aminopeptidase 2
A
291Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: map (mapB)
EC: 3.4.11.18
Find proteins for P9WK19 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WK19
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 49.330α = 90.00
b = 48.241β = 95.17
c = 56.653γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
HKL-2000data reduction
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-18
    Type: Initial release
  • Version 1.1: 2014-04-16
    Type: Other
  • Version 1.2: 2015-02-04
    Type: Database references