2NXN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

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
  • Structures With Same Primary Citation

  • 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 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: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11B147Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplKrpl11
Find proteins for P36238 (Thermus thermophilus)
Explore P36238 
Go to UniProtKB:  P36238
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.844α = 90
b = 132.844β = 90
c = 46.006γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
COMOphasing
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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