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Conserved domains on  [gi|229299796|gb|ACQ55499|]
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dicer-1, partial [Anopheles coluzzii]

Protein Classification

PAZ domain-containing protein( domain architecture ID 11671)

PAZ (Piwi Argonaut and Zwille) domain-containing protein similar to PAZ domain region of argonaute proteins which play central roles in RNA silencing processes, as essential components of the RNA-induced silencing complex (RISC) that is responsible for the gene silencing phenomenon known as RNA interference (RNAi)

Gene Ontology:  GO:0005515|GO:0003676
PubMed:  14615802|12414724

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PAZ super family cl00301
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 1-45 5.46e-27

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.


The actual alignment was detected with superfamily member cd02843:

Pssm-ID: 469713  Cd Length: 122  Bit Score: 99.83  E-value: 5.46e-27
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 229299796   1 NYATFEEYYHRKYKIHIQNQRQPLLDVDHTSARLNFLTPRYVNRK 45
Cdd:cd02843   78 EYETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 1-99 4.04e-10

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: 55.66  E-value: 4.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229299796    1 NYATFEEYYHRKYKIHIQNQRQPLLDVdhtsarlnfltpryvnrkgvalptsseetKRAKRenleqKQILVPELCTIhpf 80
Cdd:pfam02170  60 KEITVVDYFKKKYNIDLKYPDQPLLLV-----------------------------GKKRP-----KVYLPPELCNL--- 102

                          90
                  ....*....|....*....
gi 229299796   81 PASLWRAAVCLPCVLYRIN 99
Cdd:pfam02170 103 VDGQRYTKKLMPSIAQRTR 121
 
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 ...
 1-45 5.46e-27

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: 99.83  E-value: 5.46e-27
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 229299796   1 NYATFEEYYHRKYKIHIQNQRQPLLDVDHTSARLNFLTPRYVNRK 45
Cdd:cd02843   78 EYETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 4-103 1.59e-17

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: 75.79  E-value: 1.59e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229299796     4 TFEEYYHRKYKIHIQNQRQPLLdVDHTSARlnfltpRYVNRKGvalptsseetkrakrenleQKQILVPELCTIHPFPAS 83
Cdd:smart00949  65 TFVEYYKQKYNITIRDPNQPLL-VSRPKRR------RNQNGKG-------------------EPVLLPPELCFITGLTDR 118

                           90       100
                   ....*....|....*....|
gi 229299796    84 LWRAAVCLPCVLYRINALLL 103
Cdd:smart00949 119 MRKDFMLMKSIADRTRLSPL 138
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 1-99 4.04e-10

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: 55.66  E-value: 4.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229299796    1 NYATFEEYYHRKYKIHIQNQRQPLLDVdhtsarlnfltpryvnrkgvalptsseetKRAKRenleqKQILVPELCTIhpf 80
Cdd:pfam02170  60 KEITVVDYFKKKYNIDLKYPDQPLLLV-----------------------------GKKRP-----KVYLPPELCNL--- 102

                          90
                  ....*....|....*....
gi 229299796   81 PASLWRAAVCLPCVLYRIN 99
Cdd:pfam02170 103 VDGQRYTKKLMPSIAQRTR 121
 
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 ...
 1-45 5.46e-27

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: 99.83  E-value: 5.46e-27
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 229299796   1 NYATFEEYYHRKYKIHIQNQRQPLLDVDHTSARLNFLTPRYVNRK 45
Cdd:cd02843   78 EYETFEEYYKKKYKLDIQNLNQPLLDVDHTSTRLNLLTPRYVNQK 122
PAZ smart00949
This domain is named PAZ after the proteins Piwi Argonaut and Zwille; This domain is found in ...
 4-103 1.59e-17

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: 75.79  E-value: 1.59e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229299796     4 TFEEYYHRKYKIHIQNQRQPLLdVDHTSARlnfltpRYVNRKGvalptsseetkrakrenleQKQILVPELCTIHPFPAS 83
Cdd:smart00949  65 TFVEYYKQKYNITIRDPNQPLL-VSRPKRR------RNQNGKG-------------------EPVLLPPELCFITGLTDR 118

                           90       100
                   ....*....|....*....|
gi 229299796    84 LWRAAVCLPCVLYRINALLL 103
Cdd:smart00949 119 MRKDFMLMKSIADRTRLSPL 138
PAZ pfam02170
PAZ domain; This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain ...
 1-99 4.04e-10

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: 55.66  E-value: 4.04e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229299796    1 NYATFEEYYHRKYKIHIQNQRQPLLDVdhtsarlnfltpryvnrkgvalptsseetKRAKRenleqKQILVPELCTIhpf 80
Cdd:pfam02170  60 KEITVVDYFKKKYNIDLKYPDQPLLLV-----------------------------GKKRP-----KVYLPPELCNL--- 102

                          90
                  ....*....|....*....
gi 229299796   81 PASLWRAAVCLPCVLYRIN 99
Cdd:pfam02170 103 VDGQRYTKKLMPSIAQRTR 121
PAZ_CAF_like cd02844
PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has ...
 2-81 4.55e-08

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: 50.11  E-value: 4.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 229299796   2 YATFEEYYHRKYKIHIQNQRQPLLDVDHTSARLNFLTPRYVNrkgvalpTSSEETKRAKRENLEqkqiLVPELCTIHPFP 81
Cdd:cd02844   67 YATYAEYFKEKYGIVLNHPNQPLLKGKQIFNLHNLLHNRFEE-------KGESEEKEKDRYFVE----LPPELCSVIDLP 135
PAZ_piwi_like cd02845
PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be ...
 4-75 1.99e-05

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: 42.25  E-value: 1.99e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 229299796   4 TFEEYYHRKYKIHIQNQRQPLLdvdhtsarlnfltpryvnrkgvalptSSEETKRAKRENLEQKQILVPELC 75
Cdd:cd02845   66 TFVEYYKKQYNIEITDLNQPLL--------------------------VSRPKRRDPRGGEKEPIYLIPELC 111
PAZ cd02825
PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two ...
 2-43 2.48e-05

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: 42.06  E-value: 2.48e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 229299796   2 YATFEEYYHRKYKIHIQNQRQPLLDVDHTSA--RLNFLTPRYVN 43
Cdd:cd02825   70 EITFADYFKERYNLTLTDLNQPLLIVKFSSKksYSILLPPELCV 113
 
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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