Summary: RNA ligase
RNA ligase Provide feedback
This is a family of RNA ligases. The enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes.
Nandakumar J, Shuman S, Lima CD; , Cell. 2006;127:71-84.: RNA ligase structures reveal the basis for RNA specificity and conformational changes that drive ligation forward. PUBMED:17018278 EPMC:17018278
Internal database links
|Similarity to PfamA using HHSearch:||DNA_ligase_A_M|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR021122
This entry represents the RNA ligase domain. RNA ligase enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes [PUBMED:17018278]. Members of this RNA ligase family include:
- RNA editing ligase 1 (REL1) , which is essential for RNA editing and may be active in U-deletion editing [PUBMED:15465048, PUBMED:12748175, PUBMED:14536071].
- RNA editing ligase 2 (REL2), which may be active in U-insertion editing [PUBMED:14536071].
- RnlB RNA ligase 2 (or Rnl2), second RNA ligase of Enterobacteria phage T4 (Bacteriophage T4); unlike RNA ligase 1, RnlB prefers doule stranded substrates [PUBMED:12228725, PUBMED:18972386].
- 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
- the number of residues in the sequence
- the Pfam graphic itself.
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This superfamily contains both ATP-dependent and NAD dependent DNA ligase enzymes. The family also includes mRNA capping enzymes. The members of this clan were shown to be related by sequence in .
The clan contains the following 4 members:DNA_ligase_A_M DNA_ligase_aden mRNA_cap_enzyme RNA_ligase
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
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Author:||Mistry J, Coggill P|
|Number in seed:||22|
|Number in full:||428|
|Average length of the domain:||184.40 aa|
|Average identity of full alignment:||19 %|
|Average coverage of the sequence by the domain:||55.28 %|
|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:||5|
|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 RNA_ligase domain has been found. There are 7 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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