5'-3' exoribonuclease 1 isoform X6 [Mus musculus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||
| SH3_12 | pfam18129 | Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ... |
244-314 | 2.13e-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: 2.13e-26
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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 ... |
616-681 | 3.07e-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: 37.27 E-value: 3.07e-03
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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 ... |
2-77 | 9.21e-03 | ||
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: 36.29 E-value: 9.21e-03
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| Name | Accession | Description | Interval | E-value | ||
| SH3_12 | pfam18129 | Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ... |
244-314 | 2.13e-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: 2.13e-26
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| DSRM_A1CF-like | cd19872 | double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ... |
616-681 | 3.07e-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: 37.27 E-value: 3.07e-03
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| XRN1_D2_D3 | pfam18334 | Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ... |
2-77 | 9.21e-03 | ||
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: 36.29 E-value: 9.21e-03
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| Name | Accession | Description | Interval | E-value | ||
| SH3_12 | pfam18129 | Xrn1 SH3-like domain; This is the C-terminal SH3-like domain which can be found in the ... |
244-314 | 2.13e-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: 2.13e-26
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| DSRM_A1CF-like | cd19872 | double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding ... |
616-681 | 3.07e-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: 37.27 E-value: 3.07e-03
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| XRN1_D2_D3 | pfam18334 | Exoribonuclease Xrn1 D2/D3 domain; This domain can be found in 5' to 3' exoribonuclease 1 ... |
2-77 | 9.21e-03 | ||
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: 36.29 E-value: 9.21e-03
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