5NCJ | pdb_00005ncj

GriE in complex with manganese, succinate and (2S,4R)-5-hydroxyleucine

• PDB DOI: https://doi.org/10.2210/pdb5NCJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces muensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-05 Released: 2017-10-04 
• Deposition Author(s): Lukat, P., Blankenfeldt, W., Mueller, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

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

• PubMed: 29163906 
• DOI: https://doi.org/10.1039/c7sc02622f
• Primary Citation 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.

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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: [e-mail].
Structure and Function of Proteins , Helmholtz Centre for Infection Research , Inhoffenstr. 7 , 38124 Braunschweig , Germany.
German Centre for Infection Research Association (DZIF) , Partner site Hannover-Braunschweig , Germany.
Sanofi Aventis Deutschland , Industriepark Höchst , 65926 Frankfurt , Germany.
Institute of Biochemistry, Biotechnology and Bioinformatics , Technische Universität Braunschweig , Spielmannstr. 7 , 38106 Braunschweig , Germany.
Department for Chemical Biology , Helmholtz Centre for Infection Research , Inhoffenstr. 7 , 38124 Braunschweig , Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.37 kDa 
• Atom Count: 4,859 
• Modeled Residue Count: 523 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine hydroxylase	A, B	268	Streptomyces muensis	Mutation(s): 0  Gene Names: griE
UniProt
Find proteins for A0A0E3URV8 (Streptomyces muensis) Explore A0A0E3URV8  Go to UniProtKB:  A0A0E3URV8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HL5	E [auth A], H [auth B]	(2S,4R)-5-hydroxyleucine C6 H13 N O3 SDCAQJCTUOFAKD-UHNVWZDZSA-N
SIN	D [auth A], G [auth B]	SUCCINIC ACID C4 H6 O4 KDYFGRWQOYBRFD-UHFFFAOYSA-N
MN	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.74	α = 90
b = 56.061	β = 112.46
c = 73.802	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-04 
Deposition Author(s): Lukat, P., Blankenfeldt, W., Mueller, R.

Revision History  

• Version 1.0: 2017-10-04
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 1.2: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-01-17
  Changes: Refinement description