3CJQ

Ribosomal protein L11 methyltransferase (PrmA) in complex with dimethylated ribosomal protein L11 in space group P212121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 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
  • Structures With Same Primary Citation

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L11 methyltransferaseA, D, G254N/AMutation(s): 0 
Gene Names: prmA
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: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11B, E, H146N/AMutation(s): 1 
Gene Names: rplKrpl11
Find proteins for P36238 (Thermus thermophilus)
Explore P36238 
Go to UniProtKB:  P36238
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A, D, G
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
2MM
Query on 2MM

Download CCD File 
B, E, H
N,N-dimethyl-L-methionine
C7 H15 N O2 S
FLEXUHXAXRFRAU-LURJTMIESA-N
 Ligand Interaction
IOD
Query on IOD

Download CCD File 
B, H
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.526α = 90
b = 164.976β = 90
c = 180.341γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance