[spout structure figure]

SPOUT+ Methyltransferases Superfamily
PROVISIONAL DATABASE
(supplementary data to the article)

please cite:

Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases

Karolina L. Tkaczuk, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Janusz M. Bujnicki

BMC Bioinformatics 2007, 8:73
(download free PDF)

Introduction

We carried out a comparative analysis of the so-called alpha/beta knot superfamily of methyltransferases, here termed SPOUT+. We identified new members, defined similarities and differences between different families and predicted functions for many uncharacterized proteins. We conducted reclassification of SPOUT+ superfamily of methyltransferases on the basis of the phylogenetic and clustering studies of identified/predicted member sequences. For more details please have a look at the reference mentioned above.

SPOUT members - crystal structures

Superposition of all SPOUT members - crystal structures (monomeric core available only) download pdb

SPOUT Superfamily representatives

name	COG	KOG	PFAM	PDB	function	alignment	profile	reference
TrmH (SpoU)	COG0566A	KOG0838	PF00588	1v2x (TrmH Thethe)	tRNA:Gm18 MTase	download aln	download profile	Anantharaman et al. 2002
RlmB (YjfH)	COG0566B	KOG0838	PF00588	1gz0 (RlmB Esccol)	23S rRNA:Gm2251 MTase	download aln	download profile	Anantharaman et al. 2002
RrmA (YsgA)	COG0566C	KOG2506	PF00588	1ipA (RrmA Thethe)	23S rRNA:Um2479 MTase	download aln	download profile	Anantharaman et al. 2002
TrmJ	COG0565	KOG2506	PF00588	NA	tRNA:Xm32 MTase	download aln	download profile	Anantharaman et al. 2002
YibK	COG0219	KOG2506	PF00588	1mxi/1j85 (Haeinf)	predicted RNA:ribose MTase	download aln	download profile	Anantharaman et al. 2002
MJ1199, APE2001	COG4080	NA	NA	NA	predicted MTase probably does NOT act on ribose	download aln	download profile	new!!! Tkaczuk et al. 2007
TM1570	COG4752	NA	NA	NA	predicted RNA:ribose MTase	download aln	download profile	Anantharaman et al. 2002
PF0315	COG1772	KOG3925	PF04407	NA	predicted RNA:ribose MTase	download aln	download profile	new!!! Tkaczuk et al. 2007
AF2226	COG1818	NA	PF02926	NA	predicted RNA:ribose MTase	download aln	download profile	Anantharaman et al. 2002
aTrm56, PF0461	COG1303	NA	PF01994	2YY8 new!!! (Pyrhor)	tRNA:Cm56 MTase	download aln	download profile	Anantharaman et al. 2002 Kuratani et al. 2008
RsmE (YggJ)	COG1385	NA	PF04452	1vhy,1nxz	16S rRNA:m3U1498 MTase	download aln	download profile	Basturea et al. 2006
PF1826, MT1	COG2106	KOG3925	PF02598	1k3r (Metthe)	predicted MTase may generate m3U or a similar product	download aln	download profile	Anantharaman et al. 2002
PF1403, PH1401	COG1901	NA	PF04013	NA	predicted MTase unknown specificity	download aln	download profile	new!!! Tkaczuk et al. 2007
RlmH (YbeA)	COG1576	NA	PF02590	1ns5 (YbeA Esccol)	new!!! - recently confirmed specificity: 23S rRNA: m3{Psi} 1915 MTase	download aln	download profile	Anantharaman et al. 2002 Ero et al. 2008 Purta et al. 2008
Nep1p	COG1756	KOG3073	PF03587	3BBD (Nep1 Metjan)	protein involved in ribosome biogenesis predicted MTase	download aln	download profile	new!!! Tkaczuk et al. 2007 Taylor et al.2008
TrmD	COG0336	NA	PF01746	1p9p (Esccol)	tRNA:m1G37 MTase	download aln	download profile	Anantharaman et al. 2002
Trm10 (YOL093W)	COG2419	KOG2967	PF01746	NA	tRNA:m1G9 MTase	download aln	download profile	Ginalski et al. 2004
PF1588 (YOR021C)	COG2428	NA	PF04252	NA	predicted MTase unknown specificity	download aln	download profile	Ginalski et al. 2004