3EGV

Ribosomal protein L11 methyltransferase (PrmA) in complex with trimethylated ribosomal protein L11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.str.2008.03.016
  • Primary Citation of Related Structures:  
    3EGV, 3CJR, 3CJS, 3CJT, 3CJQ

  • 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 th ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal protein L11 methyltransferaseA254Thermus thermophilus HB8Mutation(s): 0 
Gene Names: prmATTHA0656
EC: 2.1.1
Find proteins for Q84BQ9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q84BQ9 
Go to UniProtKB:  Q84BQ9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11B147Thermus thermophilus HB8Mutation(s): 1 
Gene Names: rpl11rplKTTHA0247
Find proteins for Q5SLP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SLP6 
Go to UniProtKB:  Q5SLP6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
IOD
Query on IOD

Download CCD File 
B
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.547α = 90
b = 134.547β = 90
c = 48.944γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-01-18
    Changes: Non-polymer description
  • Version 1.3: 2017-03-01
    Changes: Non-polymer description