SFLD - Subgroup - Methylthiotransferase

Top Level Name

⌊ Superfamily (core) Radical SAM

2QGQ (ribosomal protein S12 methylthiotransferase RimO)

		Family known
	Total	100%	<100%	Family unknown
Functional domains	14883	13188	46	1649
UniProtKB	39462	0	33646	5816
GI	71474	63141	145	8188
Structures	2
Reactions	0
Functional domains of this subgroup were last updated on June 10, 2017
New functional domains were last added to this subgroup on Oct. 7, 2014

The methylthiotransferase (MTTase) or miaB-like family is named after the (dimethylallyl)adenosine tRNA MTTase miaB protein, which catalyses a C-H to C-S bond conversion in the methylthiolation of tRNA. A related bacterial enzyme rimO performs a similar methylthiolation, but on a protein substrate. RimO acts on the ribosomal protein S12 and forms a separate MTTase subfamily. The miaB-subfamily includes mammalian CDK5 regulatory subunit-associated proteins and similar proteins in other eukaryotes. Two other subfamilies, yqeV and CDKAL1, are named after a Bacillus subtilis and a human protein, respectively. While yqeV-like proteins are found in bacteria, CDKAL1 subfamily members occur in eukaryotes and in archaebacteria. The likely MTTases from these 4 subfamilies contain an N-terminal MTTase domain, a central radical generating fold and a C-terminal TRAM domain. The N-terminal MTTase domain contains 3 cysteines that bind a second [4Fe-4S] cluster, in addition to the radical-generating [4Fe-4S] cluster, which could be involved in the thiolation reaction. The C-terminal TRAM domain is not shared with other radical SAM proteins outside the MTTase family. The TRAM domain can bind to RNA substrate and seems to be important for substrate recognition.

Lee KH, Saleh L, Anton BP, Madinger CL, Benner JS, Iwig DF, Roberts RJ, Krebs C, Booker SJ

Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily

▸ Abstract

RimO, encoded by the yliG gene in Escherichia coli, has been recently identified in vivo as the enzyme responsible for the attachment of a methylthio group on the beta-carbon of Asp88 of the small ribosomal protein S12 [Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 1826-1831]. To date, it is the only enzyme known to catalyze methylthiolation of a protein substrate; the four other naturally occurring methylthio modifications have been observed on tRNA. All members of the methylthiotransferase (MTTase) family, to which RimO belongs, have been shown to contain the canonical CxxxCxxC motif in their primary structures that is typical of the radical S-adenosylmethionine (SAM) family of proteins. MiaB, the only characterized MTTase, and the enzyme experimentally shown to be responsible for methylthiolation of N(6)-isopentenyladenosine of tRNA in E. coli and Thermotoga maritima, has been demonstrated to harbor two distinct [4Fe-4S] clusters. Herein, we report in vitro biochemical and spectroscopic characterization of RimO. We show by analytical and spectroscopic methods that RimO, overproduced in E. coli in the presence of iron-sulfur cluster biosynthesis proteins from Azotobacter vinelandii, contains one [4Fe-4S](2+) cluster. Reconstitution of this form of RimO (RimO(rcn)) with (57)Fe and sodium sulfide results in a protein that contains two [4Fe-4S](2+) clusters, similar to MiaB. We also show by mass spectrometry that RimO(rcn) catalyzes the attachment of a methylthio group to a peptide substrate analogue that mimics the loop structure bearing aspartyl 88 of the S12 ribosomal protein from E. coli. Kinetic analysis of this reaction shows that the activity of RimO(rcn) in the presence of the substrate analogue does not support a complete turnover. We discuss the possible requirement for an assembled ribosome for fully active RimO in vitro. Our findings are consistent with those of other enzymes that catalyze sulfur insertion, such as biotin synthase, lipoyl synthase, and MiaB.

Biochemistry 2009;48(42):10162-10174 | PubMed ID: 19736993

Maiocco SJ, Arcinas AJ, Landgraf BJ, Lee KH, Booker SJ, Elliott SJ

Transformations of the FeS clusters of the methylthiotransferases MiaB and RimO, detected by direct electrochemistry

▸ Abstract

Biochemistry 2016;None(None):None-None | PubMed ID: 27598886

4 "clades": -- RimO; MiaB; YqeV and Mjo867

Static File Downloads

File Name	Description	Parameters	Stats
repnet.sg1061.th50.pE20.mek250.xgmml	Representative network: each node is a group of similar sequences	node similarity threshold = 50 max edge count = 250 min -log10 E = 20	size = 79M num_edges = 250000 num_nodes = 765
sfld_alignment_sg1061.msa	Annotated Sequence Alignment, Stockholm format		206 sequences size: 180K

Subgroup ▸ Legend	T	K	C	U	S
┗ Level: Subgroup	T	K	c		S
┗ Family	T	K	c		S

methylthiotransferase	14883	13234	13188	1649	2
┗ (dimethylallyl)adenosine tRNA methylthiotransferase (MiaB-like)	5191	5191	5179		0
┗ CDK5RAP1	903	903	903		0
┗ ribosomal protein S12 methylthiotransferase (RimO-like)	4165	4165	4143		2
┗ threonylcarbamoyladenosine tRNA methylthiotransferase	2975	2975	2963		0