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175  structures 19883  species 13  interactions 135803  sequences 139  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 12 families and the total number of domains in the clan is 135803. 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 12 member families:

DUF2122 EMG1 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...

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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) 76510 (56.3%) View
Methyltrans_RNA (PF04452) 20155 (14.8%) View
tRNA_m1G_MT (PF01746) 20072 (14.8%) View
SPOUT_MTase (PF02590) 15809 (11.6%) View
EMG1 (PF03587) 882 (0.6%) View
Methyltrn_RNA_3 (PF02598) 785 (0.6%) View
Methyltrn_RNA_2 (PF04013) 511 (0.4%) View
RNA_Me_trans (PF04252) 395 (0.3%) View
Trm56 (PF01994) 289 (0.2%) View
Methyltrn_RNA_4 (PF09936) 274 (0.2%) View
DUF2122 (PF09895) 76 (0.1%) View
SPOUT_MTase_2 (PF14419) 45 (0.0%) View
Total: 12 Total: 135803 Clan alignment
 

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Family relationships

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

Species distribution

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

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Interactions

There are 13 interactions for this clan. More...

Interacting families
A B
EMG1 EMG1
Methyltrans_RNA Methyltrans_RNA
Methyltrn_RNA_2 Methyltrn_RNA_2
Methyltrn_RNA_3 Methyltrn_RNA_3
SpoU_methylase SpoU_methylas_C
SpoU_methylase
SpoU_sub_bind
TSNR_N
SpoU_sub_bind SpoU_methylase
SPOUT_MTase SPOUT_MTase
Trm56 Trm56
tRNA_m1G_MT tRNA_m1G_MT
TSNR_N SpoU_methylase

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.

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