2YXL

Crystal Structure of PH0851

Summary for 2YXL

• Entry DOI: 10.2210/pdb2yxl/pdb
• Descriptor: 450aa long hypothetical fmu protein, SINEFUNGIN (3 entities in total)
• Functional Keywords: fmu-homolog, methyltransferase, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, transferase
• Biological source: Pyrococcus horikoshii
• Total number of polymer chains: 1
• Total formula weight: 52100.49

Authors

Hikida, Y.,Kuratani, M.,Bessho, Y.,Ishii, R.,Sekine, S.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2007-04-26, release date: 2008-04-29, Last modification date: 2023-10-25)

Primary citation

Hikida, Y.,Kuratani, M.,Bessho, Y.,Sekine, S.,Yokoyama, S.
Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase
Acta Crystallogr.,Sect.D, 66:1301-1307, 2010

PubMed Abstract: One of the modified nucleosides that frequently occurs in rRNAs and tRNAs is 5-methylcytidine (m⁵C). Escherichia coli Fmu/RsmB/RrmB is an S-adenosyl-L-methionine (AdoMet)-dependent methyltransferase that forms m⁵C967 in 16S rRNA. Fmu/RsmB/RrmB homologues exist not only in bacteria but also in archaea and eukarya and constitute a large orthologous group in the RNA:m⁵C methyltransferase family. In the present study, the crystal structure of a homologue of E. coli Fmu/RsmB/RrmB from the archaeon Pyrococcus horikoshii (PH0851) complexed with an AdoMet analogue was determined at 2.55 Å resolution. The structure and sequence of the C-terminal catalytic domain are highly conserved compared with those of E. coli Fmu/RsmB/RrmB. In contrast, the sequence of the N-terminal domain is negligibly conserved between the bacterial and archaeal subfamilies. Nevertheless, the N-terminal domains of PH0851 and E. coli Fmu/RsmB/RrmB are both α-helical and adopt a similar topology. Next to the AdoMet-binding site, a positively charged cleft is formed between the N- and C-terminal domains. This cleft is conserved in the archaeal PH0851 homologues and seems to be suitable for binding the RNA substrate.

PubMed: 21123870
DOI: 10.1107/S0907444910037558

Experimental method

X-RAY DIFFRACTION (2.55 Å)