5NCI

GriE in complex with cobalt, alpha-ketoglutarate and l-leucine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.755 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biosynthesis of methyl-proline containing griselimycins, natural products with anti-tuberculosis activity.

Lukat, P.Katsuyama, Y.Wenzel, S.Binz, T.Konig, C.Blankenfeldt, W.Bronstrup, M.Muller, R.

(2017) Chem Sci 8: 7521-7527

  • DOI: 10.1039/c7sc02622f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Griselimycins (GMs) are depsidecapeptides with superb anti-tuberculosis activity. They contain up to three (2S,4R)-4-methyl-prolines (4-MePro), of which one blocks oxidative degradation and increases metabolic stability in animal models. The natural ...

    Griselimycins (GMs) are depsidecapeptides with superb anti-tuberculosis activity. They contain up to three (2S,4R)-4-methyl-prolines (4-MePro), of which one blocks oxidative degradation and increases metabolic stability in animal models. The natural congener with this substitution is only a minor component in fermentation cultures. We showed that this product can be significantly increased by feeding the reaction with 4-MePro and we investigated the molecular basis of 4-MePro biosynthesis and incorporation. We identified the GM biosynthetic gene cluster as encoding a nonribosomal peptide synthetase and a sub-operon for 4-MePro formation. Using heterologous expression, gene inactivation, and in vitro experiments, we showed that 4-MePro is generated by leucine hydroxylation, oxidation to an aldehyde, and ring closure with subsequent reduction. The crystal structures of the leucine hydroxylase GriE have been determined in complex with substrates and products, providing insight into the stereospecificity of the reaction.


    Organizational Affiliation

    Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Helmholtz Center for Infection Research and Pharmaceutical Biotechnology , Saarland University Campus , Building C2.3 , 66123 Saarbr├╝cken , Germany . Email: Rolf.Mueller@helmholtz-hzi.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Leucine hydroxylase
A, B
268Streptomyces muensisMutation(s): 0 
Gene Names: griE
Find proteins for A0A0E3URV8 (Streptomyces muensis)
Go to UniProtKB:  A0A0E3URV8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A, B
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
LEU
Query on LEU

Download SDF File 
Download CCD File 
A, B
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.755 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.140 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 148.720α = 90.00
b = 56.061β = 111.95
c = 73.534γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references