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IPR013520 is a Ribonuclease H-like domain.
<p>This entry includes a variety of exonuclease proteins, such as Oligoribonuclease, ribonuclease T [[cite:PUB00004421]] and the epsilon subunit of DNA polymerase III.</p> <p>Ribonuclease T ([ec:3.1.13]) is an enzyme found so far only in gamma-subdivision proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a UV-repair defect caused by deletion of three other single-stranded DNA exonucleases [[cite:PUB00017662]].</p> <p>Oligoribonuclease (Orn) is an essential 3'->5' exoribonuclease in Escherichia coli and other bacteria, specialising in the degradation of small oligoribonucleotides (2-5 nucleotides) to mononucleotides during mRNA decay. It ensures complete RNA turnover by hydrolysing these short RNA fragments, which accumulate lethally in its absence, disrupting cellular viability. Beyond mRNA processing, Orn plays a critical role in cyclic diguanylate (c-di-GMP) signalling by degrading the intermediate 5'-phosphoguanylyl-(3',5')-guanosine (pGpG), preventing its accumulation and subsequent inhibition of c-di-GMP phosphodiesterases. This activity regulates biofilm formation and virulence in pathogens like Pseudomonas aeruginosa. Structurally conserved across domains of life, Orn operates processively via a manganese-dependent mechanism, preferring substrates with free 3'-hydroxyl groups and exhibiting inverse activity dependence on oligomer length. Its dual role in RNA metabolism and signalling underscores its importance in maintaining cellular homeostasis [[cite:PUB00121666], [cite:PUB00160781], [cite:PUB00053942]].</p>
This description is obtained from EB-eye REST.
| Transcript | Name | Description | Predicted domains | Domain count |
|---|---|---|---|---|
| – | PREDICTED: RNA exonuclease 4-like [Glycine max] gi|356556710|ref|XP_003546666.1| | 7 | ||
| – | PREDICTED: oligoribonuclease-like [Cicer arietinum] gi|502098281|ref|XP_004491197.1| | 10 | ||
| – | PREDICTED: RNA exonuclease 4-like [Glycine max] gi|356549691|ref|XP_003543225.1| | 17 | ||
| – | PREDICTED: RNA exonuclease 4-like [Glycine max] gi|356542307|ref|XP_003539610.1| | 9 | ||
| – | PREDICTED: small RNA degrading nuclease 5-like [Glycine max] gi|356552761|ref|XP_003544731.1| | 12 | ||
| – | PREDICTED: small RNA degrading nuclease 5-like [Glycine max] gi|356552761|ref|XP_003544731.1| | 11 | ||
| – | PREDICTED: small RNA degrading nuclease 5-like [Glycine max] gi|356552761|ref|XP_003544731.1| | 14 | ||
| – | PREDICTED: small RNA degrading nuclease 3-like [Glycine max] gi|356563578|ref|XP_003550038.1| | 10 | ||
| – | DNA polymerase III polC-type [Medicago truncatula] gi|357511765|ref|XP_003626171.1| | 10 | ||
| – | DNA polymerase III polC-type [Medicago truncatula] gi|357511765|ref|XP_003626171.1| | 10 | ||
| – | PREDICTED: RNA exonuclease 4-like [Glycine max] gi|356556710|ref|XP_003546666.1| | 12 | ||
| – | Histone mRNA exonuclease 1 [Zea mays] gi|195621024|gb|ACG32342.1| | 7 | ||
| – | Histone mRNA exonuclease 1 [Zea mays] gi|195621024|gb|ACG32342.1| | 10 | ||
| – | ERI1 exoribonuclease [Medicago truncatula] gi|357515343|ref|XP_003627960.1| | 10 | ||
| – | Exonuclease family protein [Arabidopsis lyrata subsp]. lyrata] gi|297797093|ref|XP_002866431.1| | 9 | ||
| – | DNA polymerase III polC-type [Medicago truncatula] gi|357519533|ref|XP_003630055.1| | 10 | ||
| – | Oligoribonuclease; TAIR: AT2G26970.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q9ZVE0|ORN_ARATH Oligoribonuclease; TrEMBL-Plants: tr|A0A151U1P3|A0A151U1P3_CAJCA Oligoribonuclease; Found in the gene: LotjaGi1g1v0055000 | 12 | ||
| – | Small RNA degrading nuclease; TAIR: AT5G25800.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q8L7M4|SDN5_ARATH Small RNA degrading nuclease 5; TrEMBL-Plants: tr|I1LXA9|I1LXA9_SOYBN Uncharacterized protein; Found in the gene: LotjaGi1g1v0167200 | 12 | ||
| – | Small RNA degrading nuclease; TAIR: AT5G25800.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q8L7M4|SDN5_ARATH Small RNA degrading nuclease 5; TrEMBL-Plants: tr|I1LXA9|I1LXA9_SOYBN Uncharacterized protein; Found in the gene: LotjaGi1g1v0167200 | 11 | ||
| – | Small RNA degrading nuclease; TAIR: AT5G25800.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q8L7M4|SDN5_ARATH Small RNA degrading nuclease 5; TrEMBL-Plants: tr|I1LXA9|I1LXA9_SOYBN Uncharacterized protein; Found in the gene: LotjaGi1g1v0167200 | 11 | ||
| – | RNA exonuclease 4; TAIR: AT3G27970.1 Exonuclease family protein; Swiss-Prot: sp|Q9GZR2|REXO4_HUMAN RNA exonuclease 4; TrEMBL-Plants: tr|A0A0R0EJ11|A0A0R0EJ11_SOYBN Uncharacterized protein; Found in the gene: LotjaGi1g1v0607200 | 15 | ||
| – | RNA exonuclease 4; TAIR: AT3G27970.1 Exonuclease family protein; Swiss-Prot: sp|Q9GZR2|REXO4_HUMAN RNA exonuclease 4; TrEMBL-Plants: tr|A0A151QYX1|A0A151QYX1_CAJCA RNA exonuclease 4; Found in the gene: LotjaGi1g1v0607200 | 11 | ||
| – | RNA exonuclease 4; TAIR: AT3G27970.1 Exonuclease family protein; Swiss-Prot: sp|Q9GZR2|REXO4_HUMAN RNA exonuclease 4; TrEMBL-Plants: tr|A0A0S3RW52|A0A0S3RW52_PHAAN Uncharacterized protein; Found in the gene: LotjaGi1g1v0607200 | 14 | ||
| – | Small RNA degrading nuclease; TAIR: AT5G67240.3 small RNA degrading nuclease 3; Swiss-Prot: sp|Q8RXK2|SDN3_ARATH Small RNA degrading nuclease 3; TrEMBL-Plants: tr|I3SLN1|I3SLN1_LOTJA Uncharacterized protein; Found in the gene: LotjaGi1g1v0680300 | 12 | ||
| – | DNA polymerase III polC-type; TAIR: AT5G26940.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q682U6|DPD1_ARATH Exonuclease DPD1, chloroplastic/mitochondrial; TrEMBL-Plants: tr|A0A151TW26|A0A151TW26_CAJCA DNA polymerase III polC-type; Found in the gene: LotjaGi1g1v0746900 | 11 | ||
| – | DNA polymerase III polC-type; TAIR: AT5G26940.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q682U6|DPD1_ARATH Exonuclease DPD1, chloroplastic/mitochondrial; TrEMBL-Plants: tr|A0A151TW26|A0A151TW26_CAJCA DNA polymerase III polC-type; Found in the gene: LotjaGi1g1v0746900 | 11 | ||
| – | DNA polymerase III polC-type; TAIR: AT5G26940.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q682U6|DPD1_ARATH Exonuclease DPD1, chloroplastic/mitochondrial; TrEMBL-Plants: tr|G7KWH7|G7KWH7_MEDTR DNA polymerase III, epsilon subunit-like protein; Found in the gene: LotjaGi1g1v0746900 | 11 | ||
| – | RNA exonuclease-like protein; TAIR: AT3G27970.1 Exonuclease family protein; Swiss-Prot: sp|Q9GZR2|REXO4_HUMAN RNA exonuclease 4; TrEMBL-Plants: tr|A0A0B2RL39|A0A0B2RL39_GLYSO RNA exonuclease 4; Found in the gene: LotjaGi3g1v0024300 | 14 | ||
| – | RNA exonuclease-like protein; TAIR: AT3G27970.1 Exonuclease family protein; Swiss-Prot: sp|Q9GZR2|REXO4_HUMAN RNA exonuclease 4; TrEMBL-Plants: tr|A0A0B2RL39|A0A0B2RL39_GLYSO RNA exonuclease 4; Found in the gene: LotjaGi3g1v0024300 | 14 | ||
| – | Polynucleotidyl transferase ribonuclease H-like superfamily protein; TAIR: AT3G15140.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q8W566|Y3514_ARATH Uncharacterized exonuclease domain-containing protein At3g15140; TrEMBL-Plants: tr|A0A1J7HBM7|A0A1J7HBM7_LUPAN Uncharacterized protein; Found in the gene: LotjaGi3g1v0044500 | 10 | ||
| – | Polynucleotidyl transferase ribonuclease H-like superfamily protein; TAIR: AT3G15140.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q8W566|Y3514_ARATH Uncharacterized exonuclease domain-containing protein At3g15140; TrEMBL-Plants: tr|A0A1J7HBM7|A0A1J7HBM7_LUPAN Uncharacterized protein; Found in the gene: LotjaGi3g1v0044500 | 12 | ||
| – | Polynucleotidyl transferase ribonuclease H-like superfamily protein; TAIR: AT3G15140.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q8W566|Y3514_ARATH Uncharacterized exonuclease domain-containing protein At3g15140; TrEMBL-Plants: tr|A0A1J7HBM7|A0A1J7HBM7_LUPAN Uncharacterized protein; Found in the gene: LotjaGi3g1v0044500 | 10 | ||
| – | RNA exonuclease 4; TAIR: AT3G15080.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q91560|REXO4_XENLA RNA exonuclease 4; TrEMBL-Plants: tr|A0A151R8G2|A0A151R8G2_CAJCA RNA exonuclease 4; Found in the gene: LotjaGi3g1v0155200 | 14 | ||
| – | ERI1 exoribonuclease 2; TAIR: AT3G15140.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q5HZL1|ERI2_XENLA ERI1 exoribonuclease 2; TrEMBL-Plants: tr|I1M0N0|I1M0N0_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0315800 | 11 | ||
| – | ERI1 exoribonuclease 2; TAIR: AT3G15140.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q5HZL1|ERI2_XENLA ERI1 exoribonuclease 2; TrEMBL-Plants: tr|I1M0N0|I1M0N0_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0315800 | 11 | ||
| – | ERI1 exoribonuclease 2; TAIR: AT3G15140.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q5HZL1|ERI2_XENLA ERI1 exoribonuclease 2; TrEMBL-Plants: tr|I1M0N0|I1M0N0_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0315800 | 11 | ||
| – | ERI1 exoribonuclease 2; TAIR: AT3G15140.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q5HZL1|ERI2_XENLA ERI1 exoribonuclease 2; TrEMBL-Plants: tr|I1M0N0|I1M0N0_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0315800 | 11 | ||
| – | APOLLO; TAIR: AT5G61390.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|Q0V842|NEN2_ARATH Protein NEN2; TrEMBL-Plants: tr|A0A072URH4|A0A072URH4_MEDTR Ribonuclease H superfamily polynucleotidyl transferase; Found in the gene: LotjaGi4g1v0250800 | 10 | ||
| – | Exonuclease, DNA polymerase III, epsilon subunit family; TAIR: AT4G39810.1 Polynucleotidyl transferase, ribonuclease H-like superfamily protein; Swiss-Prot: sp|F4JJ23|NEN4_ARATH Protein NEN4; TrEMBL-Plants: tr|G7LAD2|G7LAD2_MEDTR Ribonuclease H superfamily polynucleotidyl transferase; Found in the gene: LotjaGi4g1v0400200 | 11 | ||
| – | Small RNA degrading nuclease; TAIR: AT5G67240.1 small RNA degrading nuclease 3; Swiss-Prot: sp|Q8RXK2|SDN3_ARATH Small RNA degrading nuclease 3; TrEMBL-Plants: tr|I3SLN1|I3SLN1_LOTJA Uncharacterized protein; Found in the gene: LotjaGi5g1v0008300 | 12 | ||
| – | Small RNA degrading nuclease; TAIR: AT5G67240.1 small RNA degrading nuclease 3; Swiss-Prot: sp|Q8RXK2|SDN3_ARATH Small RNA degrading nuclease 3; TrEMBL-Plants: tr|I3SLN1|I3SLN1_LOTJA Uncharacterized protein; Found in the gene: LotjaGi5g1v0008300 | 12 |
A list of co-occurring predicted domains within the L. japonicus gene space:
| Predicted domain | Source | Observations | Saturation (%) |
|---|---|---|---|
| cd06145 | CDD | 1 | 2.44 |