Endoribonuclease XendoU

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

XendoU
	the structure of xendou: a splicing independent snorna processing endoribonuclease
Identifiers
Symbol	XendoU
Pfam	PF09412
InterPro	IPR018998
Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

Last updated December 23, 2020

In molecular biology, Endoribonuclease XendoU refers to a protein domain. This particular entry represents endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis (African clawed frog). This protein domain belongs to a family of evolutionarily related proteins. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini.

Function

The endonuclease, XendoU, is highly involved in the biosynthesis of a specific subclass of Xenopus laevis encoded small nucleolar RNAs (snoRNA) which are a large family of non-coding RNAs with essential roles in ribosome biogenesis. Most snoRNAs are encoded in introns and are released through the splicing reaction. Others, instead, produced by an alternative pathway consisting of endonucleolytic processing of pre-mRNA. XendoU, is the endoribonuclease responsible for this activity.^[1]

The XendoU-RNA complex is manganese (Mn²⁺)-independent. This infers that RNA binding and processing activities can be functionally separated since ions are essential for cleavage.^[2]

Structure

XendoU is a single-domain protein with roughly globular shape. It contains nine alpha helices and three antiparallel beta sheets; the latter are clustered on one side of the protein.^[1]

Homology

XendoU has no homology to any known cellular RNase. However, it has sequence similarity with proteins tentatively annotated as serine proteases.^[2]

Related Research Articles

The nucleolus is the largest structure in the nucleus of eukaryotic cells. It is best known as the site of ribosome biogenesis. Nucleoli also participate in the formation of signal recognition particles and play a role in the cell's response to stress. Nucleoli are made of proteins, DNA and RNA and form around specific chromosomal regions called nucleolar organizing regions. Malfunction of nucleoli can be the cause of several human conditions called "nucleolopathies" and the nucleolus is being investigated as a target for cancer chemotherapy.

Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of snoRNA, the C/D box snoRNAs, which are associated with methylation, and the H/ACA box snoRNAs, which are associated with pseudouridylation. SnoRNAs are commonly referred to as guide RNAs but should not be confused with the guide RNAs that direct RNA editing in trypanosomes.

U23 belongs to the H/ACA class of snoRNAs. snoRNAs bind a number of proteins to form snoRNP complexes. This class are thought to guide the sites of modification of uridines to pseudouridines by forming direct base pairing interactions with substrate RNAs. Targets include ribosomal and spliceosomal RNAs as well as the Trypanosoma spliced leader RNA as possibly other, still unknown cellular RNAs. U23 can direct the pseudouridylation of U97 in human 18S rRNA. U23 is encoded within intron 12 of the nucleolin gene in human, mouse, rat chicken, and Xenopus laevis.

SNORD15 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U16 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

SNORD18 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U22 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

SNORD29 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U34 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U35 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U36 is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U46 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U56 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U58 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U62 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U63 is a non-coding RNA (ncRNA) molecule which functions in the modification of other small nuclear RNAs (snRNAs). This type of modifying RNA is usually located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

snoRNA U73 is a non-coding RNA (ncRNA) molecule which functions in the biogenesis (modification) of other small nuclear RNAs (snRNAs). This type of modifying RNA is located in the nucleolus of the eukaryotic cell which is a major site of snRNA biogenesis. It is known as a small nucleolar RNA (snoRNA) and also often referred to as a guide RNA.

Small nucleolar RNA SNORD86 is a non-coding RNA (ncRNA) that belongs to the C/D family of snoRNAs. It is the human orthologue of Xenopus laevis U86 and has no identified RNA target. The snoRNAs U86, U56, U57 and HBII-55,of the C/D family, and the H/ACA box snoRNA ACA51 share the same host gene (NOL5A) with U86.

U8 small nucleolar RNA is the RNA component of a small RNA:protein complex which is required for biogenesis of mature large subunit ribosomal RNAs, 5.8S and 28S rRNAs.

rRNA 2'-O-methyltransferase fibrillarin is an enzyme that in humans is encoded by the FBL gene.

References

1 2 Renzi F, Caffarelli E, Laneve P, Bozzoni I, Brunori M, Vallone B (2006). "The structure of the endoribonuclease XendoU: From small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication". Proc Natl Acad Sci U S A. 103 (33): 12365–70. Bibcode:2006PNAS..10312365R. doi:10.1073/pnas.0602426103. PMC 1567885 . PMID 16895992.
1 2 Gioia U, Laneve P, Dlakic M, Arceci M, Bozzoni I, Caffarelli E (2005). "Functional characterization of XendoU, the endoribonuclease involved in small nucleolar RNA biosynthesis". J Biol Chem. 280 (19): 18996–9002. doi: 10.1074/jbc.M501160200 . PMID 15755742.

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[pmid16895992-1] 1 2 Renzi F, Caffarelli E, Laneve P, Bozzoni I, Brunori M, Vallone B (2006). "The structure of the endoribonuclease XendoU: From small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication". Proc Natl Acad Sci U S A. 103 (33): 12365–70. Bibcode:2006PNAS..10312365R. doi:10.1073/pnas.0602426103. PMC 1567885 . PMID 16895992.

[pmid15755742-2] 1 2 Gioia U, Laneve P, Dlakic M, Arceci M, Bozzoni I, Caffarelli E (2005). "Functional characterization of XendoU, the endoribonuclease involved in small nucleolar RNA biosynthesis". J Biol Chem. 280 (19): 18996–9002. doi: 10.1074/jbc.M501160200 . PMID 15755742.

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