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
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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
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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
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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
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Cellular component | cytoplasm (GO:0005737) |
Molecular function | tRNA methyltransferase activity (GO:0008175) |
Biological process | tRNA nucleoside ribose methylation (GO:0002128) |
Domain organisation
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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 13 members:
DUF2122 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_MTAlignments
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Seed (83) |
Full (256) |
Representative proteomes | UniProt (1411) |
NCBI (1413) |
Meta (75) |
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RP15 (44) |
RP35 (114) |
RP55 (238) |
RP75 (407) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (83) |
Full (256) |
Representative proteomes | UniProt (1411) |
NCBI (1413) |
Meta (75) |
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RP15 (44) |
RP35 (114) |
RP55 (238) |
RP75 (407) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Enright A |
Previous IDs: | DUF127; |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Enright A |
Number in seed: | 83 |
Number in full: | 256 |
Average length of the domain: | 118.30 aa |
Average identity of full alignment: | 50 % |
Average coverage of the sequence by the domain: | 62.97 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 119 | ||||||||||||
Family (HMM) version: | 17 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
There is 1 interaction for this family. More...
Trm56Structures
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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