3CJS

Minimal Recognition Complex between PrmA and Ribosomal Protein L11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Multiple-Site Trimethylation of Ribosomal Protein L11 by the PrmA Methyltransferase.

Demirci, H.Gregory, S.T.Dahlberg, A.E.Jogl, G.

(2008) Structure 16: 1059-1066

  • DOI: https://doi.org/10.1016/j.str.2008.03.016
  • Primary Citation of Related Structures:  
    3CJQ, 3CJR, 3CJS, 3CJT, 3EGV

  • PubMed Abstract: 

    Ribosomal protein L11 is a universally conserved component of the large subunit, and plays a significant role during initiation, elongation, and termination of protein synthesis. In Escherichia coli, the lysine methyltransferase PrmA trimethylates the N-terminal alpha-amino group and the epsilon-amino groups of Lys3 and Lys39. Here, we report four PrmA-L11 complex structures in different orientations with respect to the PrmA active site. Two structures capture the L11 N-terminal alpha-amino group in the active site in a trimethylated post-catalytic state and in a dimethylated state with bound S-adenosyl-L-homocysteine. Two other structures show L11 in a catalytic orientation to modify Lys39 and in a noncatalytic orientation. The comparison of complex structures in different orientations with a minimal substrate recognition complex shows that the binding mode remains conserved in all L11 orientations, and that substrate orientation is brought about by the unusual interdomain flexibility of PrmA.


  • Organizational Affiliation

    Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11 methyltransferase59Thermus thermophilusMutation(s): 0 
Gene Names: prmA
EC: 2.1.1
UniProt
Find proteins for Q84BQ9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q84BQ9 
Go to UniProtKB:  Q84BQ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84BQ9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11
B, C
72Thermus thermophilusMutation(s): 0 
Gene Names: rplKrpl11
UniProt
Find proteins for P36238 (Thermus thermophilus)
Explore P36238 
Go to UniProtKB:  P36238
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36238
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.211α = 90
b = 33.948β = 131.76
c = 71.09γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description