5E8J

Crystal structure of mRNA cap guanine-N7 methyltransferase in complex with RAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM.

Varshney, D.Petit, A.P.Bueren-Calabuig, J.A.Jansen, C.Fletcher, D.A.Peggie, M.Weidlich, S.Scullion, P.Pisliakov, A.V.Cowling, V.H.

(2016) Nucleic Acids Res. 44: 10423-10436

  • DOI: 10.1093/nar/gkw637
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Maturation and translation of mRNA in eukaryotes requires the addition of the 7-methylguanosine cap. In vertebrates, the cap methyltransferase, RNA guanine-7 methyltransferase (RNMT), has an activating subunit, RNMT-Activating Miniprotein (RAM). Here ...

    Maturation and translation of mRNA in eukaryotes requires the addition of the 7-methylguanosine cap. In vertebrates, the cap methyltransferase, RNA guanine-7 methyltransferase (RNMT), has an activating subunit, RNMT-Activating Miniprotein (RAM). Here we report the first crystal structure of the human RNMT in complex with the activation domain of RAM. A relatively unstructured and negatively charged RAM binds to a positively charged surface groove on RNMT, distal to the active site. This results in stabilisation of a RNMT lobe structure which co-evolved with RAM and is required for RAM binding. Structure-guided mutagenesis and molecular dynamics simulations reveal that RAM stabilises the structure and positioning of the RNMT lobe and the adjacent α-helix hinge, resulting in optimal positioning of helix A which contacts substrates in the active site. Using biophysical and biochemical approaches, we observe that RAM increases the recruitment of the methyl donor, AdoMet (S-adenosyl methionine), to RNMT. Thus we report the mechanism by which RAM allosterically activates RNMT, allowing it to function as a molecular rheostat for mRNA cap methylation.


    Organizational Affiliation

    Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRNA cap guanine-N7 methyltransferase
A, B
312Homo sapiensMutation(s): 0 
Gene Names: RNMT (KIAA0398)
EC: 2.1.1.56
Find proteins for O43148 (Homo sapiens)
Go to Gene View: RNMT
Go to UniProtKB:  O43148
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RNMT-activating mini protein
C, D
44Homo sapiensMutation(s): 0 
Gene Names: RAMAC (C15orf18, FAM103A1, RAMMET)
Find proteins for Q9BTL3 (Homo sapiens)
Go to UniProtKB:  Q9BTL3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.210 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 49.147α = 90.06
b = 50.487β = 92.41
c = 84.579γ = 115.41
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-10-14 
  • Released Date: 2016-07-13 
  • Deposition Author(s): Petit, P., Cowling, V.

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-03
    Type: Database references
  • Version 1.2: 2016-12-14
    Type: Database references
  • Version 1.3: 2019-02-20
    Type: Advisory, Data collection, Derived calculations