Protein Family Models

This entry represents a ferredoxin-like domain found in methyltransferases RsmB, RsmF and related sequences [1-5]. Paper describing PDB structure 1ixk. [1]. 14997580. Crystal structure of human p120 homologue protein PH1374 from Pyrococcus horikoshii. Ishikawa I, Sakai N, Tamura T, Yao M, Watanabe N, Tanaka I;. Proteins. 2004;54:814-816. Paper describing PDB structure 1sqf. [2]. 14656444. The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. Foster PG, Nunes CR, Greene P, Moustakas D, Stroud RM;. Structure. 2003;11:1609-1620. Paper describing PDB structure 2frx. [3]. 16793063. The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. Hallberg BM, Ericsson UB, Johnson KA, Andersen NM, Douthwaite S, Nordlund P, Beuscher AE 4th, Erlandsen H;. J Mol Biol. 2006;360:774-787. Paper describing PDB structure 2yxl. [4]. 21123870. Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase. Hikida Y, Kuratani M, Bessho Y, Sekine SI, Yokoyama S;. Acta Crystallogr D Biol Crystallogr. 2010;66:1301-1307. Paper describing PDB structure 5zvd. [5]. 30541086. Archaeal NSUN6 catalyzes m5C72 modification on a wide-range of specific tRNAs. Li J, Li H, Long T, Dong H, Wang ED, Liu RJ;. Nucleic Acids Res. 2019;47:2041-2055. (from Pfam)

Date:

2024-10-16

This family appears to have methyltransferase activity. (from Pfam)

Date:

2024-08-14

This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesised that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping [2]. [1]. 10983982. RNA methylation under heat shock control. Bugl H, Fauman EB, Staker BL, Zheng F, Kushner SR, Saper MA, Bardwell JC, Jakob U;. Mol Cell 2000;6:349-360. [2]. 8385698. Computer-assisted identification of a putative methyltransferase domain in NS5 protein of flaviviruses and lambda 2 protein of reovirus. Koonin EV;. J Gen Virol 1993;74:733-740. (from Pfam)

Date:

2024-10-16

This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme [1,2]. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA [1,2]. [1]. 14997580. Crystal structure of human p120 homologue protein PH1374 from Pyrococcus horikoshii. Ishikawa I, Sakai N, Tamura T, Yao M, Watanabe N, Tanaka I;. Proteins. 2004;54:814-816. [2]. 20558545. Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus. Demirci H, Larsen LH, Hansen T, Rasmussen A, Cadambi A, Gregory ST, Kirpekar F, Jogl G;. RNA. 2010;16:1584-1596. (from Pfam)

Date:

2024-10-16

The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. NMR structure. [1]. 9670024. Solution structure of the antitermination protein NusB of Escherichia coli: a novel all-helical fold for an RNA-binding protein. Huenges M, Rolz C, Gschwind R, Peteranderl R, Berglechner F, Richter G, Bacher A, Kessler H,Gemmecker G;. EMBO J 1998;17:4092-4100. (from Pfam)

Date:

2024-10-16

Date:

2024-08-14

This protein is also known as sun protein. The reading frame was originally interpreted as two reading frames, fmu and fmv. The recombinant protein from E. coli was shown to methylate only C967 of small subunit (16S) ribosomal RNA and to produce only m5C at that position. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.

Gene:

rsmB

Date:

2024-05-28

Catalyzes the methylation of the C5 position of C967 of the 16S rRNA

Gene:

rsmB

Date:

2021-07-30