Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 25.23 kDa 
• Atom Count: 1640 
• Residue Count: 75 
• Unique nucleic acid chains: 1

6Y3G

Crystal structure of phenylalanine tRNA from Escherichia coli

• DOI: 10.2210/pdb6Y3G/pdb
• NDB: 6Y3G

• Classification: RNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-02-18 Released: 2020-12-30 
• Deposition Author(s): Bourgeois, G., Mechulam, Y., Schmitt, E.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 

Literature

Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates.

Bourgeois, G., Seguin, J., Babin, M., Gondry, M., Mechulam, Y., Schmitt, E.

(2020) RNA 26: 1589-1602

• PubMed: 32680846 
• DOI: 10.1261/rna.075184.120
• Primary Citation of Related Structures:  
  6Y3G, 6Y4B


• PubMed Abstract: 
  

Cyclodipeptide synthases (CDPSs) catalyze the synthesis of various cyclodipeptides by using two aminoacyl-tRNA (aa-tRNA) substrates in a sequential mechanism. Here, we studied binding of phenylalanyl-tRNA ^Phe to the CDPS from Candidatus Glomeribacter gigasporarum ( Cglo -CDPS) by gel filtration and electrophoretic mobility shift assay. We determined the crystal structure of the Cglo -CDPS:Phe-tRNA ^Phe complex to 5 Å resolution and further studied it in solution using small-angle X-ray scattering (SAXS). The data show that the major groove of the acceptor stem of the aa-tRNA interacts with the enzyme through the basic β2 and β7 strands of CDPSs belonging to the XYP subfamily. A bending of the CCA extremity enables the amino acid moiety to be positioned in the P1 pocket while the terminal A76 adenosine occupies the P2 pocket. Such a positioning indicates that the present structure illustrates the binding of the first aa-tRNA. In cells, CDPSs and the elongation factor EF-Tu share aminoacylated tRNAs as substrates. The present study shows that CDPSs and EF-Tu interact with opposite sides of tRNA. This may explain how CDPSs hijack aa-tRNAs from canonical ribosomal protein synthesis.

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Organizational Affiliation: 

Laboratoire de Biologie Structurale de la Cellule, BIOC, Ecole polytechnique, CNRS, Institut Polytechnique de Paris, 91128 Palaiseau cedex, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (75-MER)	F	76	Escherichia coli

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
GAI	F	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N
CA	F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.236 
• R-Value Work: 0.215 
• R-Value Observed: 0.216 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.618	α = 90
b = 109.618	β = 90
c = 138.518	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-02-18 
• Released Date: 2020-12-30 
Deposition Author(s): Bourgeois, G., Mechulam, Y., Schmitt, E.

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Funding Organization	Location	Grant Number
French National Research Agency	France	14CE090021

Revision History 

• Version 1.0: 2020-12-30
  Type: Initial release