4Q24 | pdb_00004q24

Crystal structure of Cyclo(L-leucyl-L-phenylalanyl) synthase

• PDB DOI: https://doi.org/10.2210/pdb4Q24/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Streptomyces noursei
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-04-07 Released: 2014-10-08 
• Deposition Author(s): Moutiez, M., Schmitt, E., Seguin, J., Thai, R., Favry, E., Mechulam, Y., Gondry, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.253 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Unravelling the mechanism of non-ribosomal peptide synthesis by cyclodipeptide synthases.

Moutiez, M., Schmitt, E., Seguin, J., Thai, R., Favry, E., Belin, P., Mechulam, Y., Gondry, M.

(2014) Nat Commun 5: 5141-5141

• PubMed: 25284085 
• DOI: https://doi.org/10.1038/ncomms6141
• Primary Citation Related Structures: 
  4Q24


• PubMed Abstract: 
  

  Cyclodipeptide synthases form cyclodipeptides from two aminoacyl transfer RNAs. They use a ping-pong mechanism that begins with transfer of the aminoacyl moiety of the first aminoacyl tRNA onto a conserved serine, yielding an aminoacyl enzyme. Combining X-ray crystallography, site-directed mutagenesis and affinity labelling of the cyclodipeptide synthase AlbC, we demonstrate that the covalent intermediate reacts with the aminoacyl moiety of the second aminoacyl tRNA, forming a dipeptidyl enzyme, and identify the aminoacyl-binding sites of the aminoacyl tRNAs.

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Organizational Affiliation: 
• Service d'Ingénierie Moléculaire des Protéines, iBiTec-S, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), 91191 Gif-sur-Yvette, France.
Laboratoire de Biochimie, Unité mixte de Recherche 7654, Ecole Polytechnique, Centre National de la Recherche Scientifique, 91120 Palaiseau, France.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.23 kDa 
• Atom Count: 1,804 
• Modeled Residue Count: 224 
• Deposited Residue Count: 247 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclo(L-leucyl-L-phenylalanyl) synthase	A	247	Streptomyces noursei	Mutation(s): 1  Gene Names: albC EC: 2.3.2.20
UniProt
Find proteins for Q8GED7 (Streptomyces noursei) Explore Q8GED7  Go to UniProtKB:  Q8GED7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XVE	B [auth A]	PHENYLMETHYL N-[(2S)-4-CHLORO-3-OXO-1-PHENYL-BUTAN-2-YL]CARBAMATE C18 H18 Cl N O3 OYHLRJGDELITAF-INIZCTEOSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.253 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.968	α = 90
b = 86.968	β = 90
c = 70.738	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Moutiez, M., Schmitt, E., Seguin, J., Thai, R., Favry, E., Mechulam, Y., Gondry, M.

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary