1UWV

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

Summary for 1UWV

• Entry DOI: 10.2210/pdb1uwv/pdb
• Descriptor: 23S RRNA (URACIL-5-)-METHYLTRANSFERASE RUMA, IRON/SULFUR CLUSTER, NICKEL (II) ION, ... (6 entities in total)
• Functional Keywords: methyltransferase, rna modification, iron-sulfur cluster, transferase, rna processing
• Biological source: ESCHERICHIA COLI
• Total number of polymer chains: 1
• Total formula weight: 49276.32

Authors

Lee, T.T.,Agarwalla, S.,Stroud, R.M. (deposition date: 2004-02-11, release date: 2004-03-18, Last modification date: 2024-10-23)

Primary citation

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

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 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.

PubMed: 15016356
DOI: 10.1016/J.STR.2004.02.009

Experimental method

X-RAY DIFFRACTION (1.95 Å)