The crystal structure of E. coli Fmu binary complex with S-Adenosylmethionine at 2.1 A resolution

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.231 

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The First Structure of an RNA m5C Methyltransferase, Fmu, Provides Insight into Catalytic Mechanism and Specific Binding of RNA Substrate

Foster, P.G.Nunes, C.R.Greene, P.Moustakas, D.Stroud, R.M.

(2003) Structure 11: 1609-1620

  • DOI: https://doi.org/10.1016/j.str.2003.10.014
  • Primary Citation of Related Structures:  
    1SQF, 1SQG

  • PubMed Abstract: 

    The crystal structure of E. coli Fmu, determined at 1.65 A resolution for the apoenzyme and 2.1 A resolution in complex with AdoMet, is the first representative of the 5-methylcytosine RNA methyltransferase family that includes the human nucleolar proliferation-associated protein p120. Fmu contains three subdomains which share structural homology to DNA m(5)C methyltransferases and two RNA binding protein families. In the binary complex, the AdoMet cofactor is positioned within the active site near a novel arrangement of two conserved cysteines that function in cytosine methylation. The site is surrounded by a positively charged cleft large enough to bind its unique target stem loop within 16S rRNA. Docking of this stem loop RNA into the structure followed by molecular mechanics shows that the Fmu structure is consistent with binding to the folded RNA substrate.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, CA 94148, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUN protein429Escherichia coliMutation(s): 0 
Find proteins for P36929 (Escherichia coli (strain K12))
Explore P36929 
Go to UniProtKB:  P36929
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36929
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SAM

Download Ideal Coordinates CCD File 
C15 H22 N6 O5 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.407α = 90
b = 49.282β = 109.47
c = 86.92γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations