6QE5

Structure of E.coli RlmJ in complex with the natural cofactor product S-adenosyl-homocysteine (SAH)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

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This is version 1.1 of the entry. See complete history


Literature

Bisubstrate analogues as structural tools to investigate m6A methyltransferase active sites.

Oerum, S.Catala, M.Atdjian, C.Brachet, F.Ponchon, L.Barraud, P.Iannazzo, L.Droogmans, L.Braud, E.Etheve-Quelquejeu, M.Tisne, C.

(2019) RNA Biol 16: 798-808

  • DOI: 10.1080/15476286.2019.1589360
  • Primary Citation of Related Structures:  
    6QDX, 6QE0, 6QE5, 6QE6

  • PubMed Abstract: 
  • RNA methyltransferases (MTases) catalyse the transfer of a methyl group to their RNA substrates using most-often S-adenosyl-L-methionine (SAM) as cofactor. Only few RNA-bound MTases structures are currently available due to the difficulties in crystallising RNA:protein complexes ...

    RNA methyltransferases (MTases) catalyse the transfer of a methyl group to their RNA substrates using most-often S-adenosyl-L-methionine (SAM) as cofactor. Only few RNA-bound MTases structures are currently available due to the difficulties in crystallising RNA:protein complexes. The lack of complex structures results in poorly understood RNA recognition patterns and methylation reaction mechanisms. On the contrary, many cofactor-bound MTase structures are available, resulting in well-understood protein:cofactor recognition, that can guide the design of bisubstrate analogues that mimic the state at which both the substrate and the cofactor is bound. Such bisubstrate analogues were recently synthesized for proteins monomethylating the N6-atom of adenine (m 6 A). These proteins include, amongst others, RlmJ in E. coli and METLL3:METT14 and METTL16 in human. As a proof-of-concept, we here test the ability of the bisubstrate analogues to mimic the substrate:cofactor bound state during catalysis by studying their binding to RlmJ using differential scanning fluorimetry, isothermal titration calorimetry and X-ray crystallography. We find that the methylated adenine base binds in the correct pocket, and thus these analogues could potentially be used broadly to study the RNA recognition and catalytic mechanism of m 6 A MTases. Two bisubstrate analogues bind RlmJ with micro-molar affinity, and could serve as starting scaffolds for inhibitor design against m 6 A RNA MTases. The same analogues cause changes in the melting temperature of the m 1 A RNA MTase, TrmK, indicating non-selective protein:compound complex formation. Thus, optimization of these molecular scaffolds for m 6 A RNA MTase inhibition should aim to increase selectivity, as well as affinity.


    Organizational Affiliation

    a Laboratoire d'Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS , Université Paris Diderot , Paris , France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribosomal RNA large subunit methyltransferase JA, B300Escherichia coli PCN033Mutation(s): 0 
Gene Names: yhiRrlmJPPECC33_03818
EC: 2.1.1.266
UniProt
Find proteins for P37634 (Escherichia coli (strain K12))
Explore P37634 
Go to UniProtKB:  P37634
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH Binding MOAD:  6QE5 Kd: 7500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.218α = 79.58
b = 46.224β = 77.59
c = 71.361γ = 70.35
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Database references