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4  structures 255  species 0  interactions 271  sequences 2  architectures

Family: Trm56 (PF01994)

Summary: tRNA ribose 2'-O-methyltransferase, aTrm56

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tRNA ribose 2'-O-methyltransferase, aTrm56 Provide feedback

This family is an aTrm56 that catalyses the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Biochemical assays showed that aTrm56 forms a dimer and prefers the L-shaped tRNA to the lambda form as its substrate [1] [2]. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot for AdoMet binding, and a unique C-terminal beta-hairpin [3].

Literature references

  1. Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A;, RNA. 2005;11:1051-1063.: The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. PUBMED:15987815 EPMC:15987815

  2. Clouet-d'Orval B, Gaspin C, Mougin A;, Biochimie. 2005;87:889-895.: Two different mechanisms for tRNA ribose methylation in Archaea: a short survey. PUBMED:16164996 EPMC:16164996

  3. Kuratani M, Bessho Y, Nishimoto M, Grosjean H, Yokoyama S;, J Mol Biol. 2008;375:1064-1075.: Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA. PUBMED:18068186 EPMC:18068186

This tab holds annotation information from the InterPro database.

InterPro entry IPR002845

This entry represents tRNA ribose 2'-O-methyltransferase aTrm56, which specifically catalyzes the AdoMet-dependent 2'-O-ribose methylation of cytidine at position 56 in tRNAs.

The crystal structure of Pyrococcus horikoshii aTrm56 complexed with S-adenosyl-L-methionine has been determined to 2.48 A resolution. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot, and a unique C-terminal beta-hairpin [ PUBMED:18068186 ].

A conserved cytidine at position 56 of tRNA contributes to the maintenance of the L-shaped tertiary structure. aTrm56 catalyzes the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Biochemical assays showed that aTrm56 forms a dimer and prefers the L-shaped tRNA to the lambda form as its substrate [ PUBMED:15987815 , PUBMED:16164996 ].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan SPOUT (CL0098), which has the following description:

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.

The clan contains the following 14 members:

DUF2122 DUF531 EMG1 Methyltrans_RNA Methyltrn_RNA_2 Methyltrn_RNA_3 Methyltrn_RNA_4 RNA_Me_trans SpoU_methylas_C SpoU_methylase SPOUT_MTase SPOUT_MTase_2 Trm56 tRNA_m1G_MT


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Curation and family details

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Seed source: Enright A
Previous IDs: DUF127;
Type: Family
Sequence Ontology: SO:0100021
Author: Enright A , Ouzounis C , Bateman A
Number in seed: 81
Number in full: 271
Average length of the domain: 118.30 aa
Average identity of full alignment: 51 %
Average coverage of the sequence by the domain: 63.14 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.3 27.1
Noise cut-off 22.9 24.5
Model length: 119
Family (HMM) version: 19
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Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Trm56 domain has been found. There are 4 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
Q58780 View 3D Structure Click here