5E9J | pdb_00005e9j

Crystal structure of the mRNA cap guanine-N7 methyltransferase - modular lobe (416-456) deletion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.47 Å
  • R-Value Free: 
    0.264 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.236 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.238 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.5 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: https://doi.org/10.1093/nar/gkw637
  • Primary Citation of Related Structures:  
    5E8J, 5E9J, 5E9W

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
mRNA cap guanine-N7 methyltransferase,mRNA cap guanine-N7 methyltransferase
A, B
274Homo sapiensMutation(s): 0 
Gene Names: RNMTKIAA0398
EC: 2.1.1.56
UniProt & NIH Common Fund Data Resources
Find proteins for O43148 (Homo sapiens)
Explore O43148 
Go to UniProtKB:  O43148
PHAROS:  O43148
GTEx:  ENSG00000101654 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43148
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.47 Å
  • R-Value Free:  0.264 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.236 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.238 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.76α = 90
b = 114.38β = 90
c = 134.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SAHClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Database references
  • Version 1.2: 2016-12-14
    Changes: Database references
  • Version 1.3: 2017-02-08
    Changes: Data collection
  • Version 1.4: 2019-06-12
    Changes: Data collection, Structure summary
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Refinement description