FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also ...
51-313
1.47e-163
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: 477.84 E-value: 1.47e-163
FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also ...
51-313
1.47e-163
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: 477.84 E-value: 1.47e-163
XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of ...
2-250
3.37e-162
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: 473.94 E-value: 3.37e-162
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: 143.39 E-value: 2.96e-39
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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