Oligoribonuclease, mitochondrial (REXO2)
The protein contains 237 amino acids for an estimated molecular weight of 26833 Da.
3'-to-5' exoribonuclease specific for small oligoribonucleotides. Active on small (primarily </=5 nucleotides in length) single-stranded RNA and DNA oligomers. May have a role in cellular nucleotide recycling. (updated: March 4, 2015)
Protein identification was indicated in the following studies:
- Goodman and co-workers. (2013) The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 238(5), 509-518.
- Lange and co-workers. (2014) Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J Proteome Res. 13(4), 2028-2044.
- Hegedűs and co-workers. (2015) Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications. Database (Oxford) 1-8.
- Bryk and co-workers. (2017) Quantitative Analysis of Human Red Blood Cell Proteome. J Proteome Res. 16(8), 2752-2761.
- D'Alessandro and co-workers. (2017) Red blood cell proteomics update: is there more to discover? Blood Transfus. 15(2), 182-187.
Methods
The following articles were analysed to gather the proteome content of erythrocytes.
The gene or protein list provided in the studies were processed using the ID mapping API of Uniprot in September 2018. The number of proteins identified and mapped without ambiguity in these studies is indicated below.
Only Swiss-Prot entries (reviewed) were considered for protein evidence assignation.
| Publication | Identification 1 | Uniprot mapping 2 | Not mapped / Obsolete | TrEMBL | Swiss-Prot |
|---|---|---|---|---|---|
| Goodman (2013) | 2289 (gene list) | 2278 | 53 | 20599 | 2269 |
| Lange (2014) | 1234 | 1234 | 7 | 28 | 1224 |
| Hegedus (2015) | 2638 | 2622 | 0 | 235 | 2387 |
| Wilson (2016) | 1658 | 1528 | 170 | 291 | 1068 |
| d'Alessandro (2017) | 1826 | 1817 | 2 | 0 | 1815 |
| Bryk (2017) | 2090 | 2060 | 10 | 108 | 1942 |
| Chu (2018) | 1853 | 1804 | 55 | 362 | 1387 |
1 as available in the article and/or in supplementary material
2 uniprot mapping returns all protein isoforms as one entry
The compilation of older studies can be retrieved from the Red Blood Cell Collection database.
The data and differentiation stages presented below come from the proteomic study and analysis performed by our partners of the GReX consortium, more details are available in their published work.
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Biological Process
Nucleic acid phosphodiester bond hydrolysis
Nucleobase-containing compound metabolic process
Nucleotide metabolic process
RNA phosphodiester bond hydrolysis, exonucleolytic
Cellular Component
Focal adhesion
Mitochondrial intermembrane space
Mitochondrial matrix
Mitochondrion
Nucleolus
Nucleus
The reference OMIM entry for this protein is 607149
Rna exonuclease 2, s. cerevisiae, homolog of; rexo2
Rex2, s. cerevisiae, homolog of; rex2
Small fragment nuclease; sfn
DESCRIPTION
Nucleases are components of DNA and RNA metabolism that carry out functions in DNA repair, replication, and recombination and in RNA processing and degradation. SFN is a homolog of Orn, a 3-prime-to-5-prime exoribonuclease of E. coli that attacks the free 3-prime hydroxyl group on single-stranded RNA, releasing 5-prime mononucleotides in a sequential manner.CLONING
Using the E. coli Orn sequence as query, Nguyen et al. (2000) identified the REXO2 gene, which they called SFN, in an EST database and analyzed the clone. The deduced 205-amino acid protein has a calculated molecular mass of about 23.8 kD. The sequence shares about 50% identity with the E. coli Orn protein and contains 3 characteristic motifs, termed Exo I, II, and III, of the 3-prime-to-5-prime exonuclease superfamily. Four conserved negatively charged residues within the 3 Exo motifs are involved in positioning of the 2 divalent cations required for catalysis and phosphodiester bond cleavage. Nguyen et al. (2000) identified a splice variant, which they called SFN-alpha, that has an N-terminal extension with a putative consensus cleavage site motif for mitochondrial processing proteases. This variant appears to be a homolog of yeast Ynt20, which shows both RNAse and DNAse activity. Both SFN and SFN-alpha contain a consensus nuclear localization signal. Northern blot analysis revealed a 1-kb transcript expressed in all fetal and adult tissues tested, with highest levels in heart and relatively low levels in adult lymph nodes, brain, lung, liver, spleen, and thymus. Since the splice variants differ by only 2 nucleotides, Northern blot analysis could not distinguish between the transcripts. EST analysis suggested that the ratio of SFN to SFN-alpha is roughly 4 to 1. Gel filtration chromatography revealed that recombinant SFN expressed in bacterial cultures migrates as a 90-kD tetramer.GENE FUNCTION
By in vitro analysis, Nguyen et al. (2000) confirmed 3-prime-to-5-prime exonuclease activity in SFN for small (primarily 5 nucleotides or less in length) single-stranded RNA and DNA oligomers. SFN shows a broad substrate range, prefers Mn(2+) as a metal cofactor, and displays nuclease activity up to 50 degrees Celsius. Kinetic analysis indicated that SFN exhibits a similar affinity for small RNAs and DNAs, but degrades small RNAs about 4-fold more efficiently than DNA. Mutation of a conserved aspartate (asp136) to alanine abolished both nuclease activities.MAPPING
By genomic sequence analysis, Nguyen et al. (2000) mapped the REXO2 gene to chromosome 11q23.1-q23.2. ... More on the omim web site
Feb. 2, 2018: Protein entry updated
Automatic update: Uniprot description updated
Dec. 19, 2017: Protein entry updated
Automatic update: Uniprot description updated
Nov. 23, 2017: Protein entry updated
Automatic update: Uniprot description updated
June 20, 2017: Protein entry updated
Automatic update: comparative model was added.
March 16, 2016: Protein entry updated
Automatic update: OMIM entry 607149 was added.