1UWV

Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • DOI: 10.1016/j.str.2004.02.009
  • Also Cited By: 2BH2

  • PubMed Abstract: 
  • RumA catalyzes transfer of a methyl group from S-adenosylmethionine (SAM) specifically to uridine 1939 of 23S ribosomal RNA in Escherichia coli to yield 5-methyluridine. We determined the crystal structure of RumA at 1.95 A resolution. The protein is ...

    RumA catalyzes transfer of a methyl group from S-adenosylmethionine (SAM) specifically to uridine 1939 of 23S ribosomal RNA in Escherichia coli to yield 5-methyluridine. We determined the crystal structure of RumA at 1.95 A resolution. The protein is organized into three structural domains: The N-terminal domain contains sequence homology to the conserved TRAM motif and displays a five-stranded beta barrel architecture characteristic of an oligosaccharide/oligonucleotide binding fold. The central domain contains a [Fe(4)S(4)] cluster coordinated by four conserved cysteine residues. The C-terminal domain displays the typical SAM-dependent methyltransferase fold. The catalytic nucleophile Cys389 lies in a motif different from that in DNA 5-methylcytosine methyltransferases. The electrostatic potential surface reveals a predominately positively charged area that covers the concave surface of the first two domains and suggests an RNA binding mode. The iron-sulfur cluster may be involved in the correct folding of the protein or may have a role in RNA binding.


    Related Citations: 
    • Characterization of the 23 S Ribosomal RNA M5U1939 Methyltransferase from Escherichia Coli
      Agarwalla, S.,Kealey, J.T.,Santi, D.V.,Stroud, R.M.
      (2002) J.Biol.Chem. 277: 8835


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94107 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA
A
433Escherichia coli (strain K12)Gene Names: rlmD (rumA, ygcA)
EC: 2.1.1.190
Find proteins for P55135 (Escherichia coli (strain K12))
Go to UniProtKB:  P55135
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PO4
Query on PO4

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Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.938α = 90.00
b = 99.448β = 100.57
c = 58.519γ = 90.00
Software Package:
Software NamePurpose
Quantamodel building
SHARPphasing
SCALEPACKdata scaling
CCP4phasing
Quantaphasing
CNSphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance