Subsystem: tRNA splicing

This subsystem's description is:

For more information, please check out the description and the additional notes tabs, below

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Taxonomy Pattern 
Organism 
Domain
Variant [?] 
active
Poa1pRNPT*Sen2p
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tRNA splicing endonuclease is composed of Sen2p, Sen15p, Sen34p, and Sen54p; Sen34p contains the active site for tRNA 3' splice site cleavage and has similarity to Sen2p and to Archaeal tRNA splicing endonuclease

Sen2p corresponds to archaeal EndA

Variants:

1 = Archaeal
2 = Eukaryotic
3 = Minimal eukaryotic


S. pombe SEN2 orf not annotated and not in DNA????
>gi|50401620|sp|Q8TFH7|SEN2_SCHPO Probable tRNA-splicing endonuclease subunit sen2 (tRNA-intron endonuclease sen2)
MSKNHEVYKDALPISLAYPLPPIILTNPLTWIPYIYRYLFRKTPRQVQWQCQLHESDLSCVVTDSEAIKK
FWTSGFFGKGNLSRSEPTWHTRTKRSLGLLGFDEDLVAEEVTARRRFQRKQFKAQRAYRENRARERQLLL
ENGKPIPASLEEDAELPEYLTKSLKDFSRVSENPYHITSVPNVEHLQLTFPEAFFLASLGVLRINYENPN
FELLPILKLFANIVANSVALTHDYSLQQSHEDPIIEPDNKFLTELAAYFYFRQQGWVVKNGTKFSVDFLL
YKKGPVFSHAEFAILLIPCVGNKQKYNMQWHEVHCLNRVIAQVKKSLILCYVQCPSIEDFNKIWKNQASM
NEWDWAESVLRQYLIRCVTLRRWVPSRNRD

SEN15:
PSI-BLAST suggested weak connection to mammalian sequences, which are now also annotated as SEN15 in UniProt.
Cannot find a sequence in C. elegans.

S. pombe SEN15 orf not annotated:
>gi|50401481|sp|Q7LKV3|SE15_SCHPO Probable tRNA-splicing endonuclease subunit sen15 (tRNA-intron endonuclease sen15)
MQHNTFLPNDAVEEQKQNPYYGILRAVETDLRLGQRWCELKVHVLDIDLKTKRPLLSGIPVNGQLKDKLQ
YVLPLYLQETISIEFLSSVFDSMKKLSLPLVKDARGLSGDEFFLYLGIMCSDSTIVYYKITDGLIKPRQN
DEE


tRNA-intron endonuclease (EC 3.1.27.9) is a dimeric peptide in the greater Methanomicrobiales


The plant and fungal splicing pathway as described in
Englert, M., and Beier, H. 2005. Plant tRNA ligases are multifunctional enzymes that have diverged
in sequence and substrate specificity from RNA ligases of other phylogenetic origins.
Nucleic Acids Res. 33: 388-99.

pre-tRNA
|
| tRNA-splicing endonuclease
|\
| intron
|
5'-tRNA-2',3'-cyclic phosphate + HO-tRNA-3'
|
| cyclic phosphodiesterase (an activity of tRNA-splicing ligase (EC 6.5.1.3))
|
5'-tRNA-2'-P + HO-tRNA-3'
|
| GTP
|/
| kinase (activities of tRNA-splicing ligase (EC 6.5.1.3))
|\
| GDP
|
5'-tRNA-2'-P + P-tRNA-3'
|
| ATP
|/
| adenylyltrasferase (an activity of tRNA-splicing ligase (EC 6.5.1.3))
|\
| PPi
|
5'-tRNA-2'-P + App-tRNA-3'
|
| ligase (an activity of tRNA-splicing ligase (EC 6.5.1.3))
|\
| AMP
|
5'-tRNA-(2'-P)-3'-tRNA-3'
|
| NAD+
|/
| tRNA-splicing 2'-phosphotransferase (EC 2.7.-.-)
|\
| ADP-ribose 1"-2" cyclic phosphate (= Appr>p)
|
tRNA


ADP-ribose 1"-2" cyclic phosphate (= Appr>p)
|
| H2O
|/
| ADP-ribose 1'',2''-cyclic phosphate phophodiesterase
|
ADP-ribose 1"-phosphate (= Appr-1"p)
|
| H2O
|/
| ADP-ribose 1"-phosphate phophatase
|
ADP-ribose (= Appr)


The ordering of the cyclic phosphodiesterase step relative to the kinase and adenylyltransferase steps is not
deterministic. It is only necessary that the phosphodiesterase step be completed before the ligation.

Phosphotransferase reaction product was identified in:
Culver, G. M., McCraith, S. M., Zillmann, M., Kierzek, R., Michaud, N., LaReau, R. D., Turner, D. H., and Phizicky, E. M.
1993. An NAD derivative produced during transfer RNA splicing: ADP-ribose 1"-2" cyclic phosphate.
Science 261: 206-8.

The phosphotransferase homolog in Bacteria and Archaea (which I am calling RNA:NAD 2'-phosphotransferase)
is demonstrated to have similar substrate specificity, but is of unknown function (there is no candidate function
in Bacteria, and it is not universal amongst Archaea, so it is unlikely to be involved in splicing in Archaea). Note:
Steiger M. A., Kierzek, R., Turner, D. H., Phizicky, E. M. 2001. Substrate recognition by a yeast 2'-phosphotransferase
involved in tRNA splicing and by its Escherichia coli homolog. Biochemistry 40: 14098-105.