5NCI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1039/c7sc02622f
  • Primary Citation of Related Structures:  
    5NCH, 5NCI, 5NCJ

  • PubMed Abstract: 

    Griselimycins (GMs) are depsidecapeptides with superb anti-tuberculosis activity. They contain up to three (2 S ,4 R )-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 Saarbrücken , Germany . Email: [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine hydroxylase
A, B
268Streptomyces muensisMutation(s): 0 
Gene Names: griE
UniProt
Find proteins for A0A0E3URV8 (Streptomyces muensis)
Explore A0A0E3URV8 
Go to UniProtKB:  A0A0E3URV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E3URV8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
LEU
Query on LEU

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
I [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.72α = 90
b = 56.061β = 111.95
c = 73.534γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description