4DQV

Crystal structure of reductase (R) domain of non-ribosomal peptide synthetase from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Nonprocessive [2 + 2]e- off-loading reductase domains from mycobacterial nonribosomal peptide synthetases.

Chhabra, A.Haque, A.S.Pal, R.K.Goyal, A.Rai, R.Joshi, S.Panjikar, S.Pasha, S.Sankaranarayanan, R.Gokhale, R.S.

(2012) Proc.Natl.Acad.Sci.USA 109: 5681-5686

  • DOI: 10.1073/pnas.1118680109
  • Also Cited By: 4U5Q

  • PubMed Abstract: 
  • In mycobacteria, polyketide synthases and nonribosomal peptide synthetases (NRPSs) produce complex lipidic metabolites by using a thio-template mechanism of catalysis. In this study, we demonstrate that off-loading reductase (R) domain of mycobacteri ...

    In mycobacteria, polyketide synthases and nonribosomal peptide synthetases (NRPSs) produce complex lipidic metabolites by using a thio-template mechanism of catalysis. In this study, we demonstrate that off-loading reductase (R) domain of mycobacterial NRPSs performs two consecutive [2 + 2]e(-) reductions to release thioester-bound lipopeptides as corresponding alcohols, using a nonprocessive mechanism of catalysis. The first crystal structure of an R domain from Mycobacterium tuberculosis NRPS provides strong support to this mechanistic model and suggests that the displacement of intermediate would be required for cofactor recycling. We show that 4e(-) reductases produce alcohols through a committed aldehyde intermediate, and the reduction of this intermediate is at least 10 times more efficient than the thioester-substrate. Structural and biochemical studies also provide evidence for the conformational changes associated with the reductive cycle. Further, we show that the large substrate-binding pocket with a hydrophobic platform accounts for the remarkable substrate promiscuity of these domains. Our studies present an elegant example of the recruitment of a canonical short-chain dehydrogenase/reductase family member as an off-loading domain in the context of assembly-line enzymology.


    Organizational Affiliation

    National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROBABLE PEPTIDE SYNTHETASE NRP (PEPTIDE SYNTHASE)
A
478Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: nrp
Find proteins for Q10896 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  Q10896
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.229 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 59.058α = 90.00
b = 59.058β = 90.00
c = 238.988γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
PDB_EXTRACTdata extraction
SOLVEphasing
SCALEPACKdata scaling
HKL-2000data reduction
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Advisory, Refinement description