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 4DQV | pdb_00004dqv

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work: 
    0.229 (Depositor) 
  • R-Value Observed: 
    0.232 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4DQV

This is version 1.2 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 U S A 109: 5681-5686

  • DOI: https://doi.org/10.1073/pnas.1118680109
  • Primary Citation Related Structures: 
    4DQV

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 52.73 kDa 
  • Atom Count: 3,462 
  • Modeled Residue Count: 428 
  • Deposited Residue Count: 478 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROBABLE PEPTIDE SYNTHETASE NRP (PEPTIDE SYNTHASE)478Mycobacterium tuberculosisMutation(s): 0 
Gene Names: nrp, Rv0101, rv101
EC: 6 (PDB Primary Data), 2.3.1 (UniProt), 6.2.1.77 (UniProt)
UniProt
Find proteins for Q10896 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore Q10896 
Go to UniProtKB:  Q10896
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10896
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.278 (Depositor), 0.278 (DCC) 
  • R-Value Work:  0.229 (Depositor) 
  • R-Value Observed: 0.232 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.058α = 90
b = 59.058β = 90
c = 238.988γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Advisory, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary