Protein Family Models

This entry represents the ferredoxin-like domain found at the N-terminal of RmlL, referred to as NFLD domain usually fused to the THUMP domain [1]. Ribosomal RNA large subunit methyltransferase K/L from E.coli (also known as YcbY) specifically methylates the guanine in positions 2445 and 2069 of 23S rRNA before its assembly into 50S subunits [1]. Paper describing PDB structure 3v8v. [1]. 22362734. Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Wang KT, Desmolaize B, Nan J, Zhang XW, Li LF, Douthwaite S, Su XD;. Nucleic Acids Res. 2012;40:5138-5148. (from Pfam)

Date:

2024-10-16

The THUMP domain is named after after thiouridine synthases, methylases and PSUSs [1]. The THUMP domain consists of about 110 amino acid residues. This domain is found in many tRNA modification enzymes classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase [3]. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains [2-3] and was first predicted to function by delivering a variety of RNA modification enzymes to their targets [1]. Studies performed in tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase suggest that the THUMP domain captures the 3'-end of RNA but in some cases this is not applicable due to the modification patterns observed in tRNA [3]. Several THUMP-related proteins are also involved in other RNAs modifications, such as rRNA modification [3]. [1]. 11295541. THUMP - a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases. Aravind L, Koonin EV;. Trends Biochem Sci 2001;26:215-217. [2]. 16343540. Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain. Waterman DG, Ortiz-Lombardia M, Fogg MJ, Koonin EV, Antson AA;. J Mol Biol. 2006;356:97-110. [3]. 36833309. Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA. Hori H;. Genes (Basel). 2023;14:382. (from Pfam)

Date:

2024-10-16

This domain is the methyltransferase domain found in ribosomal RNA large subunit methyltransferase K/L from Escherichia coli (RmlKL), tRNA (guanine(10)-N2)-dimethyltransferase from Methanocaldococcus jannaschii and similar proteins, which have a THUMP domain at the N-terminal [1-4]. [1]. 11295541. THUMP - a predicted RNA-binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases. Aravind L, Koonin EV;. Trends Biochem Sci 2001;26:215-217. [2]. 16343540. Crystal structure of Bacillus anthracis ThiI, a tRNA-modifying enzyme containing the predicted RNA-binding THUMP domain. Waterman DG, Ortiz-Lombardia M, Fogg MJ, Koonin EV, Antson AA;. J Mol Biol. 2006;356:97-110. [3]. 17010378. Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA. Lesnyak DV, Sergiev PV, Bogdanov AA, Dontsova OA;. J Mol Biol. 2006;364:20-25. [4]. 22362734. Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Wang KT, Desmolaize B, Nan J, Zhang XW, Li LF, Douthwaite S, Su XD;. Nucleic Acids Res. 2012;40:5138-5148. (from Pfam)

Date:

2024-10-16