Summary: Putative tRNA binding domain
Putative tRNA binding domain Provide feedback
This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1)  human tyrosyl-tRNA synthetase  and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases . In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme . This domain may perform a common function in tRNA aminoacylation .
Simos G, Segref A, Fasiolo F, Hellmuth K, Shevchenko A, Mann M, Hurt EC; , EMBO J 1996;15:5437-5448.: The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl-and glutamyl-tRNA synthetases. PUBMED:8895587 EPMC:8895587
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR002547This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [PUBMED:8895587], human tyrosyl-tRNA synthetase [PUBMED:9162081], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases [PUBMED:8895587]. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme [PUBMED:8895587]. This domain may perform a common function in tRNA aminoacylation [PUBMED:9162081].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||tRNA binding (GO:0000049)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin . The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands .
The clan contains the following 45 members:BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF3127 DUF35 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_NTP_bind OB_RNB OmdA Phage_DNA_bind POT1 RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RuvA_N S1 S1-like S1_2 SSB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Pfam-B_482 (release 4.1)|
|Author:||Bashton M, Bateman A|
|Number in seed:||43|
|Number in full:||10729|
|Average length of the domain:||99.10 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||16.79 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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There are 2 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 tRNA_bind domain has been found. There are 53 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 seqence.
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