2NXN

T. thermophilus ribosomal protein L11 methyltransferase (PrmA) in complex with ribosomal protein L11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Recognition of ribosomal protein L11 by the protein trimethyltransferase PrmA.

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

(2007) Embo J. 26: 567-577

  • DOI: 10.1038/sj.emboj.7601508
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial ribosomal protein L11 is post-translationally trimethylated at multiple residues by a single methyltransferase, PrmA. Here, we describe four structures of PrmA from the extreme thermophile Thermus thermophilus. Two apo-PrmA structures at 1. ...

    Bacterial ribosomal protein L11 is post-translationally trimethylated at multiple residues by a single methyltransferase, PrmA. Here, we describe four structures of PrmA from the extreme thermophile Thermus thermophilus. Two apo-PrmA structures at 1.59 and 2.3 A resolution and a third with bound cofactor S-adenosyl-L-methionine at 1.75 A each exhibit distinct relative positions of the substrate recognition and catalytic domains, revealing how PrmA can position the L11 substrate for multiple, consecutive side-chain methylation reactions. The fourth structure, the PrmA-L11 enzyme-substrate complex at 2.4 A resolution, illustrates the highly specific interaction of the N-terminal domain with its substrate and places Lys39 in the PrmA active site. The presence of a unique flexible loop in the cofactor-binding site suggests how exchange of AdoMet with the reaction product S-adenosyl-L-homocysteine can occur without necessitating the dissociation of PrmA from L11. Finally, the mode of interaction of PrmA with L11 explains its observed preference for L11 as substrate before its assembly into the 50S ribosomal subunit.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L11 methyltransferase
A
254Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: prmA
EC: 2.1.1.-
Find proteins for Q84BQ9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q84BQ9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
B
147Thermus thermophilusMutation(s): 0 
Gene Names: rplK (rpl11)
Find proteins for P36238 (Thermus thermophilus)
Go to UniProtKB:  P36238
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 132.844α = 90.00
b = 132.844β = 90.00
c = 46.006γ = 120.00
Software Package:
Software NamePurpose
MAR345data collection
HKL-2000data scaling
COMOphasing
HKL-2000data reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-26
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description