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IPR001247

Description

IPR001247 is a Exoribonuclease, phosphorolytic domain 1.

<p>This entry represents the phosphorolytic (PH) domain 1, which has a core 2-layer α/β structure with a left-handed crossover, similar to that found in ribosomal protein S5. This domain is found in bacterial/organelle PNPases and in archaeal/eukaryotic exosomes [[cite:PUB00000954]].</p> <p>The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate.</p> <p>PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [[cite:PUB00035567]], as well as in archaeal and eukaryotic RNA exosomes [[cite:PUB00035568], [cite:PUB00035569]], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber [[cite:PUB00035570]]. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [[cite:PUB00035571], [cite:PUB00035572]].</p>

This description is obtained from EB-eye REST.

Associated GO terms

Unable to find any GO terms for the transcript with the identifier.

Associated Lotus transcripts 35

Transcript Name Description Predicted domains Domain count
PREDICTED: exosome complex component RRP43-like [Glycine max] gi|356526509|ref|XP_003531860.1| 14
PREDICTED: exosome complex component MTR3-like [Cicer arietinum] gi|502145425|ref|XP_004506024.1| 10
PREDICTED: exosome complex exonuclease RRP46 homolog isoform X1 [Cicer arietinum] gi|502105061|ref|XP_004492714.1| 9
PREDICTED: exosome complex exonuclease RRP46 homolog isoform X1 [Cicer arietinum] gi|502105061|ref|XP_004492714.1| 11
PREDICTED: probable polyribonucleotide nucleotidyltransferase 1, chloroplastic-like [Cicer arietinum] gi|502107284|ref|XP_004493216.1| 36
7
PREDICTED: exosome complex component RRP45-like isoform X3 [Cicer arietinum] gi|502122025|ref|XP_004497542.1| 14
Exosome complex exonuclease RRP46 [Medicago truncatula] gi|357507241|ref|XP_003623909.1| 11
PREDICTED: polyribonucleotide nucleotidyltransferase 2, mitochondrial-like [Cicer arietinum] gi|502090489|ref|XP_004489245.1| 33
PREDICTED: exosome complex component RRP43-like [Glycine max] gi|356526509|ref|XP_003531860.1| 10
PREDICTED: exosome complex component RRP42-like [Glycine max] gi|356559534|ref|XP_003548054.1| 9
PREDICTED: exosome complex component RRP42-like [Glycine max] gi|356559534|ref|XP_003548054.1| 9
Polyribonucleotide nucleotidyltransferase; TAIR: AT3G46210.1 Ribosomal protein S5 domain 2-like superfamily protein; Swiss-Prot: sp|Q9LX74|EXOS5_ARATH Exosome complex exonuclease RRP46 homolog; TrEMBL-Plants: tr|I3SU44|I3SU44_LOTJA Uncharacterized protein; Found in the gene: LotjaGi1g1v0474000_LC 9
Exosome complex component; TAIR: AT3G46210.1 Ribosomal protein S5 domain 2-like superfamily protein; Swiss-Prot: sp|Q9LX74|EXOS5_ARATH Exosome complex exonuclease RRP46 homolog; TrEMBL-Plants: tr|I3SU44|I3SU44_LOTJA Uncharacterized protein; Found in the gene: LotjaGi1g1v0474000_LC 12
Polyribonucleotide nucleotidyltransferase; TAIR: AT3G46210.1 Ribosomal protein S5 domain 2-like superfamily protein; Swiss-Prot: sp|Q9LX74|EXOS5_ARATH Exosome complex exonuclease RRP46 homolog; TrEMBL-Plants: tr|I3SU44|I3SU44_LOTJA Uncharacterized protein; Found in the gene: LotjaGi1g1v0474000_LC 8
Polyribonucleotide nucleotidyltransferase; TAIR: AT3G03710.1 polyribonucleotide nucleotidyltransferase; Swiss-Prot: sp|Q69LE7|PNP1_ORYSJ Probable polyribonucleotide nucleotidyltransferase 1, chloroplastic; TrEMBL-Plants: tr|G7L1J6|G7L1J6_MEDTR Polyribonucleotide nucleotidyltransferase; Found in the gene: LotjaGi1g1v0648200 36
Exosome complex component; TAIR: AT3G60500.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q9M209|CER7_ARATH Exosome complex component RRP45B; TrEMBL-Plants: tr|G7IP72|G7IP72_MEDTR Exosome complex exonuclease RRP41; Found in the gene: LotjaGi1g1v0741200 15
Ribonuclease PH; TAIR: AT3G61620.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q9SP08|RRP41_ARATH Exosome complex component RRP41 homolog; TrEMBL-Plants: tr|G7L401|G7L401_MEDTR Exosome complex exonuclease RRP41; Found in the gene: LotjaGi1g1v0789600 13
Exosome complex component; TAIR: AT3G07750.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q15024|EXOS7_HUMAN Exosome complex component RRP42; TrEMBL-Plants: tr|I3T9E4|I3T9E4_LOTJA Uncharacterized protein; Found in the gene: LotjaGi2g1v0066400 14
Exosome complex component; TAIR: AT3G07750.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q15024|EXOS7_HUMAN Exosome complex component RRP42; TrEMBL-Plants: tr|I3T9E4|I3T9E4_LOTJA Uncharacterized protein; Found in the gene: LotjaGi2g1v0066400 14
Polyribonucleotide nucleotidyltransferase; TAIR: AT3G46210.1 Ribosomal protein S5 domain 2-like superfamily protein; Swiss-Prot: sp|Q9LX74|EXOS5_ARATH Exosome complex exonuclease RRP46 homolog; TrEMBL-Plants: tr|I3SU44|I3SU44_LOTJA Uncharacterized protein; Found in the gene: LotjaGi2g1v0171400 11
Polyribonucleotide nucleotidyltransferase; TAIR: AT5G14580.1 polyribonucleotide nucleotidyltransferase; Swiss-Prot: sp|Q9S7G6|PNP2_ARATH Polyribonucleotide nucleotidyltransferase 2, mitochondrial; TrEMBL-Plants: tr|V7C0V9|V7C0V9_PHAVU Uncharacterized protein; Found in the gene: LotjaGi2g1v0243700 32
Polyribonucleotide nucleotidyltransferase; TAIR: AT5G14580.1 polyribonucleotide nucleotidyltransferase; Swiss-Prot: sp|Q9S7G6|PNP2_ARATH Polyribonucleotide nucleotidyltransferase 2, mitochondrial; TrEMBL-Plants: tr|V7C0V9|V7C0V9_PHAVU Uncharacterized protein; Found in the gene: LotjaGi2g1v0243700 35
Exosome complex component; TAIR: AT4G27490.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|A2RVK7|RP41L_ARATH Exosome complex component RRP41-like; TrEMBL-Plants: tr|I3SC00|I3SC00_LOTJA Uncharacterized protein; Found in the gene: LotjaGi2g1v0358300 14
Exosome complex component; TAIR: AT4G27490.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|A2RVK7|RP41L_ARATH Exosome complex component RRP41-like; TrEMBL-Plants: tr|I3SC00|I3SC00_LOTJA Uncharacterized protein; Found in the gene: LotjaGi2g1v0358300 14
Polyribonucleotide nucleotidyltransferase; TAIR: AT4G27490.7 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|A2RVK7|RP41L_ARATH Exosome complex component RRP41-like; TrEMBL-Plants: tr|I3SC00|I3SC00_LOTJA Uncharacterized protein; Found in the gene: LotjaGi2g1v0358300 13
Exosome complex component; TAIR: AT1G60080.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q2KHU3|EXOS8_BOVIN Exosome complex component RRP43; TrEMBL-Plants: tr|A0A151QPU2|A0A151QPU2_CAJCA Exosome complex exonuclease RRP43; Found in the gene: LotjaGi4g1v0121200 13
Exosome complex component; TAIR: AT1G60080.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q2KHU3|EXOS8_BOVIN Exosome complex component RRP43; TrEMBL-Plants: tr|A0A151QPU2|A0A151QPU2_CAJCA Exosome complex exonuclease RRP43; Found in the gene: LotjaGi4g1v0121200 13
Exosome complex component; TAIR: AT1G60080.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q2KHU3|EXOS8_BOVIN Exosome complex component RRP43; TrEMBL-Plants: tr|A0A151QPU2|A0A151QPU2_CAJCA Exosome complex exonuclease RRP43; Found in the gene: LotjaGi4g1v0121200 13
Exosome complex component; TAIR: AT3G07750.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q15024|EXOS7_HUMAN Exosome complex component RRP42; TrEMBL-Plants: tr|I3T9E4|I3T9E4_LOTJA Uncharacterized protein; Found in the gene: LotjaGi5g1v0053800 14
Exosome complex component; TAIR: AT3G07750.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q15024|EXOS7_HUMAN Exosome complex component RRP42; TrEMBL-Plants: tr|I3T9E4|I3T9E4_LOTJA Uncharacterized protein; Found in the gene: LotjaGi5g1v0053800 14
Exosome complex component; TAIR: AT1G60080.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q96B26|EXOS8_HUMAN Exosome complex component RRP43; TrEMBL-Plants: tr|I1KWF8|I1KWF8_SOYBN Uncharacterized protein; Found in the gene: LotjaGi6g1v0013300 14
Exosome complex component; TAIR: AT1G60080.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q2KHU3|EXOS8_BOVIN Exosome complex component RRP43; TrEMBL-Plants: tr|A0A151QPU2|A0A151QPU2_CAJCA Exosome complex exonuclease RRP43; Found in the gene: LotjaGi6g1v0013300 14
Exosome complex component; TAIR: AT1G60080.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q96B26|EXOS8_HUMAN Exosome complex component RRP43; TrEMBL-Plants: tr|I1MA04|I1MA04_SOYBN Uncharacterized protein; Found in the gene: LotjaGi6g1v0013300 14
Exosome complex component; TAIR: AT1G60080.1 3'-5'-exoribonuclease family protein; Swiss-Prot: sp|Q96B26|EXOS8_HUMAN Exosome complex component RRP43; TrEMBL-Plants: tr|I1KWF8|I1KWF8_SOYBN Uncharacterized protein; Found in the gene: LotjaGi6g1v0013300 14

Co-occuring domains 1

A list of co-occurring predicted domains within the L. japonicus gene space:

Predicted domain Source Observations Saturation (%)
cd11369 CDD 1 2.86