Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
112  structures 5028  species 6  interactions 32567  sequences 85  architectures

Clan: SPOUT (CL0098)

Summary

SPOUT Methyltransferase Superfamily Add an annotation

A distinct class of methylases that includes the SpoU and TrmD superfamilies and two superfamilies of predicted methylases defined by the YbeA and MJ0421 proteins in bacteria and archaea, respectively [1] (PFAM:PF00588 PFAM:PF01746). SPOUT is structurally distinct compared to more classical methyltransferases [1]. More specifically, the members of this clan form alpha/beta knots. Knots are extremely rare in protein structures as they pose a folding problem. The mechanism that allow a domain to be folded as a knot are unclear, but are discussed in [2] and reference therein. All members with known structure form homodimers.

This clan contains 11 families and the total number of domains in the clan is 32567. The clan was built by RD Finn.

Literature references

  1. Anantharaman V, Koonin EV, Aravind L;, J Mol Microbiol Biotechnol. 2002;4:71-75.: SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. PUBMED:11763972 EPMC:11763972
  2. Lim K, Zhang H, Tempczyk A, Krajewski W, Bonander N, Toedt J, Howard A, Eisenstein E, Herzberg O; , Proteins 2003;51:56-67.: Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): a cofactor bound at a site formed by a knot. PUBMED:12596263 EPMC:12596263
  3. Tkaczuk KL, Dunin-Horkawicz S, Purta E, Bujnicki JM; , BMC Bioinformatics. 2007;8:73.: Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. PUBMED:17338813 EPMC:17338813

Members

This clan contains the following 11 member families:

DUF2122 Methyltrans_RNA Methyltrn_RNA_2 Methyltrn_RNA_3 Methyltrn_RNA_4 RNA_Me_trans SpoU_methylase SPOUT_MTase SPOUT_MTase_2 Trm56 tRNA_m1G_MT

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

Loading domain graphics...

Alignments

The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
SpoU_methylase (PF00588) 17854 (54.8%) View
tRNA_m1G_MT (PF01746) 5148 (15.8%) View
Methyltrans_RNA (PF04452) 4583 (14.1%) View
SPOUT_MTase (PF02590) 3767 (11.6%) View
Methyltrn_RNA_3 (PF02598) 418 (1.3%) View
Methyltrn_RNA_2 (PF04013) 215 (0.7%) View
Methyltrn_RNA_4 (PF09936) 174 (0.5%) View
RNA_Me_trans (PF04252) 169 (0.5%) View
Trm56 (PF01994) 143 (0.4%) View
DUF2122 (PF09895) 59 (0.2%) View
SPOUT_MTase_2 (PF14419) 37 (0.1%) View
Total: 11 Total: 32567 Clan alignment
 

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

Tree controls

Hide

This tree shows the occurrence of the domains in this clan across different species. More...

Loading...

Interactions

There are 6 interactions for this clan. More...

Interacting families
A B
SpoU_methylase SpoU_methylase
SpoU_sub_bind
tRNA_m1G_MT tRNA_m1G_MT
Methyltrans_RNA Methyltrans_RNA
Methyltrn_RNA_3 Methyltrn_RNA_3
Methyltrn_RNA_2 Methyltrn_RNA_2

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

Loading structure mapping...