Protein Family Models

Radical SAM proteins catalyse diverse reactions, including unusual methylations, isomerisation, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. [1]. 11222759. Radical SAM, a novel protein superfamily linking unresolved. steps in familiar biosynthetic pathways with radical mechanisms:. functional characterization using new analysis and information. visualization methods.. Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE;. Nucleic Acids Res 2001;29:1097-1106.. [2]. 17335281. Anaerobic sulfatase-maturating enzymes: radical SAM enzymes able. to catalyze in vitro sulfatase post-translational modification.. Benjdia A, Leprince J, Guillot A, Vaudry H, Rabot S, Berteau O;. J Am Chem Soc. 2007;129:3462-3463.. [3]. 16766528. A new type of bacterial sulfatase reveals a novel maturation. pathway in prokaryotes.. Berteau O, Guillot A, Benjdia A, Rabot S;. J Biol Chem. 2006;281:22464-22470. (from Pfam)

Date:

2024-09-08

This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation). [1]. 11313137. TRAM, a predicted RNA-binding domain, common to tRNA uracil. methylation and adenine thiolation enzymes.. Anantharaman V, Koonin EV, Aravind L;. FEMS Microbiol Lett 2001;197:215-221. (from Pfam)

Date:

2024-08-14

This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins [1,2]. This domain is a nearly always found in conjunction with Pfam:PF04055 and Pfam:PF01938 although its function is uncertain. [1]. 11313137. TRAM, a predicted RNA-binding domain, common to tRNA uracil. methylation and adenine thiolation enzymes.. Anantharaman V, Koonin EV, Aravind L;. FEMS Microbiol Lett 2001;197:215-221.. [2]. 11882645. Enzymatic modification of tRNAs: MiaB is an iron-sulfur protein.. Pierrel F, Bjork GR, Fontecave M, Atta M;. J Biol Chem 2002;277:13367-13370. (from Pfam)

Date:

2024-08-14

MiaB/RimO family radical SAM methylthiotransferase similar to ribosomal protein S12 methylthiotransferase RimO, which catalyzes the methylthiolation of the residue Asp-89 of ribosomal protein S12, and tRNA-i(6)A37 methylthiotransferase (MiaB), which catalyzes the methylthiolation of N6-(dimethylallyl)adenosine (i(6)A) at position 37 in tRNAs

Date:

2024-05-06

This model represents homologs of the MiaB enzyme responsible for the modification of the isopentenylated adenine-37 base of most bacterial and eukaryotic tRNAs that read codons beginning with uracil. Adenine-37 is next to the anticodon on the 3' side in these tRNA's.

Gene:

miaB

Date:

2023-06-23

This subfamily contains the tRNA-i(6)A37 modification enzyme, MiaB (TIGR01574). The phylogenetic tree indicates 4 distinct clades, one of which corresponds to MiaB. The other three clades are modelled by hypothetical equivalogs (TIGR01125, TIGR01579 and TIGR01578). Together, the four models hit every sequence hit by the subfamily model without any overlap between them. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related.

Date:

2024-05-30