3CJT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 

Starting Models: experimental
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Ligand Structure Quality Assessment 


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: 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 methyltransferase
A, C, E, G, I
A, C, E, G, I, K, M, O
254Thermus thermophilusMutation(s): 1 
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L11
B, D, F, H, J
B, D, F, H, J, L, N, P
147Thermus 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
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
DA [auth G],
KA [auth K],
PA [auth O],
Y [auth C]
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
SAH
Query on SAH

Download Ideal Coordinates CCD File 
AA [auth E],
IA [auth I],
MA [auth M],
T [auth A]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
2MM
Query on 2MM

Download Ideal Coordinates CCD File 
CA [auth F],
JA [auth J],
NA [auth M],
W [auth B]
N,N-dimethyl-L-methionine
C7 H15 N O2 S
FLEXUHXAXRFRAU-LURJTMIESA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
U [auth A],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
BA [auth F]
EA [auth I]
FA [auth I]
LA [auth M]
OA [auth N]
BA [auth F],
EA [auth I],
FA [auth I],
LA [auth M],
OA [auth N],
Q [auth A],
V [auth B],
Z [auth E]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
GA [auth I],
HA [auth I],
R [auth A],
S [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.198 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.822α = 90
b = 69.943β = 90.47
c = 379.007γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description