2BH2

Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

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This is version 1.2 of the entry. See complete history. 


Literature

A Unique RNA Fold in the Ruma-RNA-Cofactor Ternary Complex Contributes to Substrate Selectivity and Enzymatic Function

Lee, T.T., Agarwalla, S., Stroud, R.M.

(2005) Cell 120: 599

  • DOI: 10.1016/j.cell.2004.12.037
  • Primary Citation of Related Structures:  
    2BH2

  • PubMed Abstract: 

    • A single base (U1939) within E. coli 23S ribosomal RNA is methylated by its dedicated enzyme, RumA. The structure of RumA/RNA/S-adenosylhomocysteine uncovers the mechanism for achieving unique selectivity. The single-stranded substrate is "refolded" on the enzyme into a compact conformation with six key intra-RNA interactions ...

    A single base (U1939) within E. coli 23S ribosomal RNA is methylated by its dedicated enzyme, RumA. The structure of RumA/RNA/S-adenosylhomocysteine uncovers the mechanism for achieving unique selectivity. The single-stranded substrate is "refolded" on the enzyme into a compact conformation with six key intra-RNA interactions. The RNA substrate contributes directly to catalysis. In addition to the target base, a second base is "flipped out" from the core loop to stack against the adenine of the cofactor S-adenosylhomocysteine. Nucleotides in permuted sequence order are stacked into the site vacated by the everted target U1939 and compensate for the energetic penalty of base eversion. The 3' hairpin segment of the RNA binds distal to the active site and provides binding energy that contributes to enhanced catalytic efficiency. Active collaboration of RNA in catalysis leads us to conclude that RumA and its substrate RNA may reflect features from the earliest RNA-protein era.

    Related Citations: 
    • Crystal Structure of Ruma, an Iron-Sulfur Cluster Containing E. Coli Ribosomal RNA 5-Methyluridine Methyltransferase
      Lee, T.T., Agarwalla, S., Stroud, R.M.
      (2004) Structure 12: 397
    Organizational Affiliation: 

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMAA, B433Escherichia coliMutation(s): 0 
EC: 2.1.1 (PDB Primary Data), 2.1.1.190 (UniProt)
UniProt
Find proteins for P55135 (Escherichia coli (strain K12))
Explore P55135 
Go to UniProtKB:  P55135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55135
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNA 1932-1968C, D37Escherichia coli
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]		S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.061α = 90
b = 63.542β = 125.15
c = 112.019γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance