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Conserved domains on  [gi|589911155]
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Chain A, Endoribonuclease Dicer

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 123-245 5.13e-71

PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.


:

Pssm-ID: 239209  Cd Length: 122  Bit Score: 215.39  E-value: 5.13e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589911155 123 DSSTLDIDFKF*EDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 202
Cdd:cd02843    1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 589911155 203 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 245
Cdd:cd02843   80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
 
Name Accession Description Interval E-value
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 123-245 5.13e-71

PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.


Pssm-ID: 239209  Cd Length: 122  Bit Score: 215.39  E-value: 5.13e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589911155 123 DSSTLDIDFKF*EDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 202
Cdd:cd02843    1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 589911155 203 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 245
Cdd:cd02843   80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 162-302 5.07e-29

This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.


Pssm-ID: 198017  Cd Length: 138  Bit Score: 107.76  E-value: 5.07e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589911155   162 EDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltp 239
Cdd:smart00949  25 KDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL-VSRPK-------- 91

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 589911155   240 RHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLL 302
Cdd:smart00949  92 RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 151-301 2.71e-20

PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerization. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteriztic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.


Pssm-ID: 460472  Cd Length: 123  Bit Score: 84.17  E-value: 2.71e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589911155  151 YTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 228
Cdd:pfam02170   8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 589911155  229 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 301
Cdd:pfam02170  87 ---------------------------GKK------RPKVYLPPELCN---LVDGQRYTKKLMPSIAQRTRLL 123
 
Name Accession Description Interval E-value
PAZ_dicer_like cd02843
PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA ...
 123-245 5.13e-71

PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.


Pssm-ID: 239209  Cd Length: 122  Bit Score: 215.39  E-value: 5.13e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589911155 123 DSSTLDIDFKF*EDIEkSEARIGIPSTKYTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFPSPEY 202
Cdd:cd02843    1 DSSTLDIDWEFMEKIE-ANARIGPRATPDEARQPFKFDAEDYQDAVVMPWYRNFDQPQYFYVAEICTDLRPLSKFPGPEY 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 589911155 203 ETFAEYYKTKYNLDLTNLNQPLLDVDHTSSRLNLLTPRHLNQK 245
Cdd:cd02843   80 ETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
PAZ cd02825
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 123-245 4.40e-30

PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain.


Pssm-ID: 239207  Cd Length: 115  Bit Score: 109.86  E-value: 4.40e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589911155 123 DSSTLDIDFKF*EDIEKSEARIGIPSTKYTKETPfVFKLEDYQDaviipryrnfdQPHRFYVADVYTDLTPLS--KFPSP 200
Cdd:cd02825    1 ADPVIETMCKFPKDREIDTPLLDSPREEFTKELK-GLKVEDTHN-----------PLNRVYRPDGETRLKAPSqlKHSDG 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 589911155 201 EYETFAEYYKTKYNLDLTNLNQPLLDVDHTS--SRLNLLTPRHLNQK 245
Cdd:cd02825   69 KEITFADYFKERYNLTLTDLNQPLLIVKFSSkkSYSILLPPELCVIT 115
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 162-302 5.07e-29

This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.


Pssm-ID: 198017  Cd Length: 138  Bit Score: 107.76  E-value: 5.07e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589911155   162 EDYQDAVIIPRYRNfdqpHRFYVADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdVDHTSsrlnlltp 239
Cdd:smart00949  25 KDLKGLIVLTRYNN----KTYRIDDIDWNLAPKSTFEKSDGSeiTFVEYYKQKYNITIRDPNQPLL-VSRPK-------- 91

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 589911155   240 RHLNQKGKalplssaekrkakweslQNKQILVPELCAIHPIPASLWRKAVCLPSILYRLHCLL 302
Cdd:smart00949  92 RRRNQNGK-----------------GEPVLLPPELCFITGLTDRMRKDFMLMKSIADRTRLSP 137
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 151-301 2.71e-20

PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerization. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteriztic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway.


Pssm-ID: 460472  Cd Length: 123  Bit Score: 84.17  E-value: 2.71e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589911155  151 YTKETPFVFKLEDYQDAVIIPRYRNFDQPHRFYVADVYTDLTPLSKFP--SPEYETFAEYYKTKYNLDLTNLNQPLLDVd 228
Cdd:pfam02170   8 QQQKDRRDFRKEAKKALKGLKVYTTYNNPRTYRIDGITFDPTPESTFPlkDGKEITVVDYFKKKYNIDLKYPDQPLLLV- 86

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 589911155  229 htssrlnlltprhlnqkgkalplssaeKRKakweslQNKQILVPELCAihpIPASLWRKAVCLPSILYRLHCL 301
Cdd:pfam02170  87 ---------------------------GKK------RPKVYLPPELCN---LVDGQRYTKKLMPSIAQRTRLL 123
PAZ_CAF_like cd02844
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ...
 159-281 4.22e-15

PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA molecules. PAZ domains are named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.


Pssm-ID: 239210  Cd Length: 135  Bit Score: 70.53  E-value: 4.22e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589911155 159 FKLEDYQDAVIIpryrnfdQPH--RFYVADVYTDLTPLSKFP---SPEYETFAEYYKTKYNLDLTNLNQPLLDVDHTSSR 233
Cdd:cd02844   26 FCACDLKGSVVT-------APHngRFYVISGILDLNANSSFPgkeGLGYATYAEYFKEKYGIVLNHPNQPLLKGKQIFNL 98

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 589911155 234 LNLLTPRhLNQKGkalplSSAEKRKakwesLQNKQILVPELCAIHPIP 281
Cdd:cd02844   99 HNLLHNR-FEEKG-----ESEEKEK-----DRYFVELPPELCSVIDLP 135
PAZ_piwi_like cd02845
PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be ...
 165-275 1.08e-08

PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be essential for the maintenance of germline stem cells. In the Drosophila male germline, Piwi was shown to be involved in the silencing of retrotransposons in the male gametes. The Piwi proteins share their domain architecture with other members of the argonaute family. The PAZ domain has been named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes.


Pssm-ID: 239211  Cd Length: 117  Bit Score: 52.26  E-value: 1.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 589911155 165 QDAVIIPRYRNfdqphRFY-VADVYTDLTPLSKFPSPEYE--TFAEYYKTKYNLDLTNLNQPLLdvdhtssrlnlltprh 241
Cdd:cd02845   29 IGSIVLTRYNN-----KTYrIDDIDFDKTPLSTFKKSDGTeiTFVEYYKKQYNIEITDLNQPLL---------------- 87

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 589911155 242 lnqkgkalpLSSAEKRKAKweSLQNKQI-LVPELC 275
Cdd:cd02845   88 ---------VSRPKRRDPR--GGEKEPIyLIPELC 111
 
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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