2CWW

Crystal structure of Thermus thermophilus TTHA1280, a putative SAM-dependent RNA methyltransferase, in complex with S-adenosyl-L-homocysteine

Summary for 2CWW

• Entry DOI: 10.2210/pdb2cww/pdb
• Related: 1WXW 1WXX
• Descriptor: putative SAM-dependent RNA methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, ACETIC ACID, ... (5 entities in total)
• Functional Keywords: structural genomics, sam-dependent rna methyltransferase, s-adenosyl-l-homocysteine, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, transferase
• Biological source: Thermus thermophilus
• Cellular location: Cytoplasm (By similarity): Q5SIT4
• Total number of polymer chains: 2
• Total formula weight: 87051.60

Authors

Pioszak, A.A.,Murayama, K.,Nakagawa, N.,Ebihara, A.,Kuramitsu, S.,Shirouzu, M.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2005-06-27, release date: 2005-10-11, Last modification date: 2023-10-25)

Primary citation

Pioszak, A.A.,Murayama, K.,Nakagawa, N.,Ebihara, A.,Kuramitsu, S.,Shirouzu, M.,Yokoyama, S.
Structures of a putative RNA 5-methyluridine methyltransferase, Thermus thermophilus TTHA1280, and its complex with S-adenosyl-L-homocysteine.
Acta Crystallogr.,Sect.F, 61:867-874, 2005

PubMed Abstract: The Thermus thermophilus hypothetical protein TTHA1280 belongs to a family of predicted S-adenosyl-L-methionine (AdoMet) dependent RNA methyltransferases (MTases) present in many bacterial and archaeal species. Inspection of amino-acid sequence motifs common to class I Rossmann-fold-like MTases suggested a specific role as an RNA 5-methyluridine MTase. Selenomethionine (SeMet) labelled and native versions of the protein were expressed, purified and crystallized. Two crystal forms of the SeMet-labelled apoprotein were obtained: SeMet-ApoI and SeMet-ApoII. Cocrystallization of the native protein with S-adenosyl-L-homocysteine (AdoHcy) yielded a third crystal form, Native-AdoHcy. The SeMet-ApoI structure was solved by the multiple anomalous dispersion method and refined at 2.55 A resolution. The SeMet-ApoII and Native-AdoHcy structures were solved by molecular replacement and refined at 1.80 and 2.60 A, respectively. TTHA1280 formed a homodimer in the crystals and in solution. Each subunit folds into a three-domain structure composed of a small N-terminal PUA domain, a central alpha/beta-domain and a C-terminal Rossmann-fold-like MTase domain. The three domains form an overall clamp-like shape, with the putative active site facing a deep cleft. The architecture of the active site is consistent with specific recognition of uridine and catalysis of methyl transfer to the 5-carbon position. The cleft is suitable in size and charge distribution for binding single-stranded RNA.

PubMed: 16511182
DOI: 10.1107/S1744309105029842

Experimental method

X-RAY DIFFRACTION (2.6 Å)