Summary: LigT like Phosphoesterase
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LigT like Phosphoesterase Provide feedback
Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known . They belong to the 2H phosphoesterase superfamily . They share a common active site, characterised by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins.
Hofmann A, Zdanov A, Genschik P, Ruvinov S, Filipowicz W, Wlodawer A; , EMBO J 2000;19:6207-6217.: Structure and mechanism of activity of the cyclic phosphodiesterase of Appr>p, a product of the tRNA splicing reaction. PUBMED:11080166 EPMC:11080166
Mazumder R, Iyer LM, Vasudevan S, Aravind L; , Nucleic Acids Res 2002;30:5229-5243.: Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily. PUBMED:12466548 EPMC:12466548
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR014051
This entry represents a domain found in a number of known and predicted phosphoesterases. These include bacterial and archaeal 2',5' RNA ligases, and a family of predicted phosphoesterases known as the YjcG family. The 2',5' RNA ligases perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA [PUBMED:8940112]. The physiological substrate(s) in prokaryotes may include small 2',5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. This domain contains a conserved HXTX motif which is thought to be important for catalytic activity, as it is in the related enzyme cyclic nucleotide phosphodiesterase (CPDase) [PUBMED:12466548]. In 2',5' RNA ligase this domain is duplicated, with the two conserved motifs forming the proposed active site, which is analogous to that of CPDase [PUBMED:12798681].
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This clan includes a number of phosphoesterases that contain an internal duplication.
The clan contains the following 9 members:2_5_RNA_ligase2 2H-phosphodiest AKAP7_NLS CNPase Corona_NS2A CPDase DUF1045 HVSL LigT_PEase
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Seed source:||Bateman A|
|Previous IDs:||2_5_ligase; 2_5_RNA_ligase;|
|Author:||Bateman A, Mazumder R, Anantharaman V|
|Number in seed:||107|
|Number in full:||4805|
|Average length of the domain:||79.80 aa|
|Average identity of full alignment:||44 %|
|Average coverage of the sequence by the domain:||49.00 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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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 LigT_PEase domain has been found. There are 9 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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