Summary: RNA 3'-terminal phosphate cyclase
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RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organisms. They catalyse the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate . The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids .
Palm GJ, Billy E, Filipowicz W, Wlodawer A; , Structure Fold Des 2000;8:13-23.: Crystal structure of RNA 3'-terminal phosphate cyclase, a ubiquitous enzyme with unusual topology. PUBMED:10673421 EPMC:10673421
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This tab holds annotation information from the InterPro database.
InterPro entry IPR023797
RNA cyclases are a family of RNA-modifying enzymes that are conserved in eukaryotes, bacteria and archaea. Type 1 RNA 3'-terminal phosphate cyclases (EC) [PUBMED:9184239, PUBMED:2199762] catalyse the conversion of 3'-phosphate to a 2',3'-cyclic phosphodiester at the end of RNA:
The physiological function of the cyclase is not known, but the enzyme could be involved in the maintenance of cyclic ends in tRNA splicing intermediates or in the cyclisation of the 3' end of U6 snRNA [PUBMED:9184239].
A second subfamily of RNA 3'-terminal phosphate cyclases (type 2) that do not have cyclase activity have been identified in eukaryotes. They are localised to the nucleolus and are involved in ribosomal modification [PUBMED:10790377].
The crystal structure of RNA 3'-terminal phosphate cyclase shows that each molecule consists of two domains. The larger domain contains three repeats of a folding unit comprising two parallel alpha helices and a four-stranded beta sheet; this fold was previously identified in translation initiation factor 3 (IF3). The large domain is similar to one of the two domains of 5-enolpyruvylshikimate-3-phosphate synthase and UDP-N-acetylglucosamine enolpyruvyl transferase. The smaller domain uses a similar secondary structure element with different topology, observed in many other proteins such as thioredoxin [PUBMED:10673421]. Although the active site of this enzyme has not been unambiguously assigned, it can be mapped to a region surrounding His309, an adenylate acceptor, in which a number of amino acids are highly conserved in the enzyme from different sources [PUBMED:10673421].
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|Author:||Finn RD, Bateman A|
|Number in seed:||29|
|Number in full:||1194|
|Average length of the domain:||309.70 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||89.51 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|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 RTC domain has been found. There are 19 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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