6Y4B

Structure of cyclodipeptide synthase from Candidatus Glomeribacter gigasporarum bound to Phe-tRNAPhe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.304 
  • R-Value Observed: 0.305 

wwPDB Validation   3D Report Full Report



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

  • 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 Candidat ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclodipeptide synthaseA297Candidatus Glomeribacter gigasporarum BEG34Mutation(s): 0 
Gene Names: CAGGBEG34_30028
Find proteins for G2JBB2 (Candidatus Glomeribacter gigasporarum BEG34)
Explore G2JBB2 
Go to UniProtKB:  G2JBB2
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (77-MER)F76Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHE
Query on PHE

Download Ideal Coordinates CCD File 
F
PHENYLALANINE
C9 H11 N O2
COLNVLDHVKWLRT-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.00 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.304 
  • R-Value Observed: 0.305 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 254.834α = 90
b = 254.834β = 90
c = 69.41γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance14CE090021

Revision History 

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