5'-3' exoribonuclease 1 isoform X3 [Mus musculus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||||
| XRN1 super family | cl34882 | 5'-3' exonuclease [Replication, recombination and repair]; |
1-659 | 0e+00 | ||||||||||||
5'-3' exonuclease [Replication, recombination and repair]; The actual alignment was detected with superfamily member COG5049: Pssm-ID: 227382 [Multi-domain] Cd Length: 953 Bit Score: 588.82 E-value: 0e+00
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| XRN1_D1 super family | cl39678 | Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) ... |
582-767 | 2.18e-34 | ||||||||||||
Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity. The actual alignment was detected with superfamily member pfam18332: Pssm-ID: 436418 Cd Length: 192 Bit Score: 131.06 E-value: 2.18e-34
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| SH3_12 | pfam18129 | Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ... |
1025-1095 | 4.09e-26 | ||||||||||||
Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain. : Pssm-ID: 465661 Cd Length: 68 Bit Score: 102.64 E-value: 4.09e-26
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| XRN1_D2_D3 super family | cl39680 | Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ... |
777-858 | 4.01e-04 | ||||||||||||
Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 pfam18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment pfam03159. The actual alignment was detected with superfamily member pfam18334: Pssm-ID: 436419 Cd Length: 87 Bit Score: 40.91 E-value: 4.01e-04
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| DSRM_SF super family | cl00054 | double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 ... |
1397-1462 | 4.63e-03 | ||||||||||||
double-stranded RNA binding motif (DSRM) superfamily; DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis. The actual alignment was detected with superfamily member cd19872: Pssm-ID: 444671 Cd Length: 75 Bit Score: 37.66 E-value: 4.63e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||||
| XRN1 | COG5049 | 5'-3' exonuclease [Replication, recombination and repair]; |
1-659 | 0e+00 | ||||||||||||
5'-3' exonuclease [Replication, recombination and repair]; Pssm-ID: 227382 [Multi-domain] Cd Length: 953 Bit Score: 588.82 E-value: 0e+00
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| XRN_N | pfam03159 | XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of ... |
2-223 | 1.58e-139 | ||||||||||||
XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalysing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus. Pssm-ID: 460832 [Multi-domain] Cd Length: 231 Bit Score: 429.65 E-value: 1.58e-139
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| PIN_XRN1-2-like | cd18673 | FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also ... |
32-258 | 1.60e-128 | ||||||||||||
FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also known as SEP1) is a processive 5'-3' exoribonuclease that degrades the body of transcripts in the major pathway of RNA decay; XRN2 (5'-3' exoribonuclease 2) is predominantly localized in the nucleus and recognizes single-stranded RNAs with a 5'-terminal monophosphate to degrade them possessively to mononucleotides. XRN2 has a critical function to process maturation of 5.8S and 25S/28S rRNAs as well as degradation of some spacer fragments that are excised during rRNA maturation. Both XRN1 and XRN2 preferentially cleave 5'-monophosphorylated RNA. XRN2 is also known as Rat1p in yeast. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Pssm-ID: 350240 Cd Length: 240 Bit Score: 400.03 E-value: 1.60e-128
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| XRN1_D1 | pfam18332 | Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) ... |
582-767 | 2.18e-34 | ||||||||||||
Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity. Pssm-ID: 436418 Cd Length: 192 Bit Score: 131.06 E-value: 2.18e-34
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| SH3_12 | pfam18129 | Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ... |
1025-1095 | 4.09e-26 | ||||||||||||
Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain. Pssm-ID: 465661 Cd Length: 68 Bit Score: 102.64 E-value: 4.09e-26
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| XRN1_D2_D3 | pfam18334 | Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ... |
777-858 | 4.01e-04 | ||||||||||||
Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 pfam18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment pfam03159. Pssm-ID: 436419 Cd Length: 87 Bit Score: 40.91 E-value: 4.01e-04
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| DSRM_A1CF-like | cd19872 | double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ... |
1397-1462 | 4.63e-03 | ||||||||||||
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding protein 46 (RBM46) and similar proteins; The family includes two dsRNA-binding motif-containing proteins, A1CF and RBM46. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. RBM46 (also called cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. Members of this family contain three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380701 Cd Length: 75 Bit Score: 37.66 E-value: 4.63e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||||
| XRN1 | COG5049 | 5'-3' exonuclease [Replication, recombination and repair]; |
1-659 | 0e+00 | ||||||||||||
5'-3' exonuclease [Replication, recombination and repair]; Pssm-ID: 227382 [Multi-domain] Cd Length: 953 Bit Score: 588.82 E-value: 0e+00
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| XRN_N | pfam03159 | XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of ... |
2-223 | 1.58e-139 | ||||||||||||
XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalysing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus. Pssm-ID: 460832 [Multi-domain] Cd Length: 231 Bit Score: 429.65 E-value: 1.58e-139
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| PIN_XRN1-2-like | cd18673 | FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also ... |
32-258 | 1.60e-128 | ||||||||||||
FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also known as SEP1) is a processive 5'-3' exoribonuclease that degrades the body of transcripts in the major pathway of RNA decay; XRN2 (5'-3' exoribonuclease 2) is predominantly localized in the nucleus and recognizes single-stranded RNAs with a 5'-terminal monophosphate to degrade them possessively to mononucleotides. XRN2 has a critical function to process maturation of 5.8S and 25S/28S rRNAs as well as degradation of some spacer fragments that are excised during rRNA maturation. Both XRN1 and XRN2 preferentially cleave 5'-monophosphorylated RNA. XRN2 is also known as Rat1p in yeast. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Pssm-ID: 350240 Cd Length: 240 Bit Score: 400.03 E-value: 1.60e-128
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| XRN_M | pfam17846 | Xrn1 helical domain; This helical domain is part of the Xrn1 catalytic core. Xrn1 is a ... |
321-517 | 7.57e-75 | ||||||||||||
Xrn1 helical domain; This helical domain is part of the Xrn1 catalytic core. Xrn1 is a cytoplasmic 5'-3' exonuclease that degrades decapped mRNAs. Pssm-ID: 375377 Cd Length: 442 Bit Score: 256.56 E-value: 7.57e-75
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| XRN1_D1 | pfam18332 | Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) ... |
582-767 | 2.18e-34 | ||||||||||||
Exoribonuclease Xrn1 D1 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity. Pssm-ID: 436418 Cd Length: 192 Bit Score: 131.06 E-value: 2.18e-34
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| PIN_FEN-like | cd09853 | FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ... |
33-251 | 2.02e-31 | ||||||||||||
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved in DNA replication, repair, and recombination; Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. Canonical members of this FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Pssm-ID: 350204 [Multi-domain] Cd Length: 174 Bit Score: 121.82 E-value: 2.02e-31
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| SH3_12 | pfam18129 | Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ... |
1025-1095 | 4.09e-26 | ||||||||||||
Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain. Pssm-ID: 465661 Cd Length: 68 Bit Score: 102.64 E-value: 4.09e-26
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| XRN1_D2_D3 | pfam18334 | Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ... |
777-858 | 4.01e-04 | ||||||||||||
Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 pfam18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment pfam03159. Pssm-ID: 436419 Cd Length: 87 Bit Score: 40.91 E-value: 4.01e-04
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| DSRM_A1CF-like | cd19872 | double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ... |
1397-1462 | 4.63e-03 | ||||||||||||
double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding protein 46 (RBM46) and similar proteins; The family includes two dsRNA-binding motif-containing proteins, A1CF and RBM46. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. RBM46 (also called cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. Members of this family contain three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure. Pssm-ID: 380701 Cd Length: 75 Bit Score: 37.66 E-value: 4.63e-03
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