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Conserved domains on  [gi|74184155|dbj|BAE37081|]
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unnamed protein product, partial [Mus musculus]

Protein Classification

XRN 5'-3' exonuclease N-terminal domain-containing protein( domain architecture ID 10504459)

XRN 5'-3' exonuclease N-terminal domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRN_N pfam03159
XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of ...
 2-109 2.37e-67

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: 201.99  E-value: 2.37e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74184155     2 GVPKFYRWISERYP-CLSEVVKEHQI--PEFDNLYLDMNGIIHQCSHPNDDdvHFRISDDKIFTDIFHYLEVLFRIIKPR 78
Cdd:pfam03159   1 GVPAFFRWLSERYPlIISQVIEESRPngKEFDNLYLDMNGIIHPCSHPEDG--PAPKTEEEMFKNIFAYIDRLFNIVRPR 78

                          90       100       110
                  ....*....|....*....|....*....|.
gi 74184155    79 KVFFMAVDGVAPRAKMNQQRGRRFRSAKEAE 109
Cdd:pfam03159  79 KLLYMAVDGVAPRAKMNQQRSRRFRSAKEAE 109
 
Name Accession Description Interval E-value
XRN_N pfam03159
XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of ...
 2-109 2.37e-67

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: 201.99  E-value: 2.37e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74184155     2 GVPKFYRWISERYP-CLSEVVKEHQI--PEFDNLYLDMNGIIHQCSHPNDDdvHFRISDDKIFTDIFHYLEVLFRIIKPR 78
Cdd:pfam03159   1 GVPAFFRWLSERYPlIISQVIEESRPngKEFDNLYLDMNGIIHPCSHPEDG--PAPKTEEEMFKNIFAYIDRLFNIVRPR 78

                          90       100       110
                  ....*....|....*....|....*....|.
gi 74184155    79 KVFFMAVDGVAPRAKMNQQRGRRFRSAKEAE 109
Cdd:pfam03159  79 KLLYMAVDGVAPRAKMNQQRSRRFRSAKEAE 109
XRN1 COG5049
5'-3' exonuclease [Replication, recombination and repair];
1-109 3.53e-50

5'-3' exonuclease [Replication, recombination and repair];


Pssm-ID: 227382 [Multi-domain]  Cd Length: 953  Bit Score: 169.33  E-value: 3.53e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74184155   1 MGVPKFYRWISERYPCLSEVVKEHQIPEFDNLYLDMNGIIHQCSHPNddDVHFRISDDKIFTDIFHYLEVLFRIIKPRKV 80
Cdd:COG5049   1 MGVPSFFRWLSERYPKIIQLIEEKQIPEFDNLYLDMNGILHNCTHPN--DGSPPETEEEMYKAVFEYIDHILLKIRPRKL 78

                        90       100
                ....*....|....*....|....*....
gi 74184155  81 FFMAVDGVAPRAKMNQQRGRRFRSAKEAE 109
Cdd:COG5049  79 LYMAVDGVAPRAKMNQQRARRFRSAKDAS 107
PIN_XRN1-2-like cd18673
FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also ...
 32-109 3.57e-45

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: 145.80  E-value: 3.57e-45
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 74184155  32 LYLDMNGIIHQCSHPNDDDvhFRISDDKIFTDIFHYLEVLFRIIKPRKVFFMAVDGVAPRAKMNQQRGRRFRSAKEAE 109
Cdd:cd18673   1 LYLDMNGIIHPCTHPEDRP--APKSEEEMFQNIFKYIDRLFNIVRPRKLLYIAVDGVAPRAKMNQQRSRRFRSAKEAE 76
 
Name Accession Description Interval E-value
XRN_N pfam03159
XRN 5'-3' exonuclease N-terminus; This family aligns residues towards the N-terminus of ...
 2-109 2.37e-67

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: 201.99  E-value: 2.37e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74184155     2 GVPKFYRWISERYP-CLSEVVKEHQI--PEFDNLYLDMNGIIHQCSHPNDDdvHFRISDDKIFTDIFHYLEVLFRIIKPR 78
Cdd:pfam03159   1 GVPAFFRWLSERYPlIISQVIEESRPngKEFDNLYLDMNGIIHPCSHPEDG--PAPKTEEEMFKNIFAYIDRLFNIVRPR 78

                          90       100       110
                  ....*....|....*....|....*....|.
gi 74184155    79 KVFFMAVDGVAPRAKMNQQRGRRFRSAKEAE 109
Cdd:pfam03159  79 KLLYMAVDGVAPRAKMNQQRSRRFRSAKEAE 109
XRN1 COG5049
5'-3' exonuclease [Replication, recombination and repair];
1-109 3.53e-50

5'-3' exonuclease [Replication, recombination and repair];


Pssm-ID: 227382 [Multi-domain]  Cd Length: 953  Bit Score: 169.33  E-value: 3.53e-50
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 74184155   1 MGVPKFYRWISERYPCLSEVVKEHQIPEFDNLYLDMNGIIHQCSHPNddDVHFRISDDKIFTDIFHYLEVLFRIIKPRKV 80
Cdd:COG5049   1 MGVPSFFRWLSERYPKIIQLIEEKQIPEFDNLYLDMNGILHNCTHPN--DGSPPETEEEMYKAVFEYIDHILLKIRPRKL 78

                        90       100
                ....*....|....*....|....*....
gi 74184155  81 FFMAVDGVAPRAKMNQQRGRRFRSAKEAE 109
Cdd:COG5049  79 LYMAVDGVAPRAKMNQQRARRFRSAKDAS 107
PIN_XRN1-2-like cd18673
FEN-like PIN domains of XRN1, XRN2, and related proteins; XRN1 (5'-3' exoribonuclease 1, also ...
 32-109 3.57e-45

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: 145.80  E-value: 3.57e-45
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 74184155  32 LYLDMNGIIHQCSHPNDDDvhFRISDDKIFTDIFHYLEVLFRIIKPRKVFFMAVDGVAPRAKMNQQRGRRFRSAKEAE 109
Cdd:cd18673   1 LYLDMNGIIHPCTHPEDRP--APKSEEEMFQNIFKYIDRLFNIVRPRKLLYIAVDGVAPRAKMNQQRSRRFRSAKEAE 76
PIN_FEN-like cd09853
FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved ...
 33-109 4.20e-15

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: 66.74  E-value: 4.20e-15
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 74184155  33 YLDMNGIIHQCSHPNDDDVHfriSDDKIFTDIFHYLEVLFRIIKPRKVFFMAVDGVAPRAKMNQQRGRRFRSAKEAE 109
Cdd:cd09853   1 VIDGMNIAFNFAHPVRNLKE---EEGSDFQGYFSAVDDLVKKLKPGIKPILLFDGGKPKAKKGNRDKRRERRAREED 74
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
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