uncharacterized subfamily of N-terminal LabA-like PIN domains; This N-terminal LabA-like PIN domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain), has been shown to play a role in cyanobacterial circadian timing. The LabA-like C-terminal domains characteristic of this subfamily may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains). The function of the N-terminal domain is unknown. The LabA-like PIN domain family also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Other members are the LabA-like PIN domains of human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349730   9 FAVLIDADNVSGKYIKCILDEVSSDGIATYKRIYGDWSSPLLQSWKSLLLDNSILPIQQYGYTTGKNATDSAMIIDAMDI 88
Cdd:cd11297    1 IAVLIDAENISASYADAILEELAKYGRVVVRRAYGDWSSPRLKGWKDELLEHGIEPIQQFSYTKGKNAADIALVIDAMDL 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 972349730  89 LYSGNVEGFYIVSSDSDFTRLAARLRESGMYVVGMGE 125
Cdd:cd11297   81 LYTGRIDTFVIVSSDSDFTPLAQRLRELGKTVIGIGE 117

uncharacterized subfamily of N-terminal LabA-like PIN domains; This N-terminal LabA-like PIN domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain), has been shown to play a role in cyanobacterial circadian timing. The LabA-like C-terminal domains characteristic of this subfamily may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains). The function of the N-terminal domain is unknown. The LabA-like PIN domain family also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Other members are the LabA-like PIN domains of human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349730   9 FAVLIDADNVSGKYIKCILDEVSSDGIATYKRIYGDWSSPLLQSWKSLLLDNSILPIQQYGYTTGKNATDSAMIIDAMDI 88
Cdd:cd11297    1 IAVLIDAENISASYADAILEELAKYGRVVVRRAYGDWSSPRLKGWKDELLEHGIEPIQQFSYTKGKNAADIALVIDAMDL 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 972349730  89 LYSGNVEGFYIVSSDSDFTRLAARLRESGMYVVGMGE 125
Cdd:cd11297   81 LYTGRIDTFVIVSSDSDFTPLAQRLRELGKTVIGIGE 117

NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349730    8 RFAVLIDADNVS---GKYIKCILDEVSSDGIATYKRIYGDWSSPLLQSWKSLLLDNSIlPIQQYGYTTGKNATDSAMIID 84
Cdd:pfam01936   1 RVAVFIDGENCPlpdGVDYRKVLEEIRSGGEVVRARAYGNWGDPDLRKFPDALSSTGI-PVQHKPLTKGKNAVDVGLAVD 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 972349730   85 AMDILYSGNVEGFYIVSSDSDFTRLAARLRESGMYVVGMG--EKKTPQPFISACNKF 139
Cdd:pfam01936  80 ALELAYDNNPDTFVLVSGDGDFAPLLERLRERGKRVEVLGaeEPSTSDALINAADRF 136

OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 972349730  192 AIRNIVeeISDEDGWAFTGELGSVLTKRYP-DFDVRNFGFKKLTPFLKSLG 241
Cdd:pfam12872   1 ELISLL--RSDPDGWASLSELGSEYRKLFGeDFDPRNYGFSKLSDLLKAIP 49

uncharacterized subfamily of N-terminal LabA-like PIN domains; This N-terminal LabA-like PIN domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain), has been shown to play a role in cyanobacterial circadian timing. The LabA-like C-terminal domains characteristic of this subfamily may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains). The function of the N-terminal domain is unknown. The LabA-like PIN domain family also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Other members are the LabA-like PIN domains of human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349730   9 FAVLIDADNVSGKYIKCILDEVSSDGIATYKRIYGDWSSPLLQSWKSLLLDNSILPIQQYGYTTGKNATDSAMIIDAMDI 88
Cdd:cd11297    1 IAVLIDAENISASYADAILEELAKYGRVVVRRAYGDWSSPRLKGWKDELLEHGIEPIQQFSYTKGKNAADIALVIDAMDL 80

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 972349730  89 LYSGNVEGFYIVSSDSDFTRLAARLRESGMYVVGMGE 125
Cdd:cd11297   81 LYTGRIDTFVIVSSDSDFTPLAQRLRELGKTVIGIGE 117

NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 972349730    8 RFAVLIDADNVS---GKYIKCILDEVSSDGIATYKRIYGDWSSPLLQSWKSLLLDNSIlPIQQYGYTTGKNATDSAMIID 84
Cdd:pfam01936   1 RVAVFIDGENCPlpdGVDYRKVLEEIRSGGEVVRARAYGNWGDPDLRKFPDALSSTGI-PVQHKPLTKGKNAVDVGLAVD 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 972349730   85 AMDILYSGNVEGFYIVSSDSDFTRLAARLRESGMYVVGMG--EKKTPQPFISACNKF 139
Cdd:pfam01936  80 ALELAYDNNPDTFVLVSGDGDFAPLLERLRERGKRVEVLGaeEPSTSDALINAADRF 136

OST-HTH/LOTUS domain; A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 972349730  192 AIRNIVeeISDEDGWAFTGELGSVLTKRYP-DFDVRNFGFKKLTPFLKSLG 241
Cdd:pfam12872   1 ELISLL--RSDPDGWASLSELGSEYRKLFGeDFDPRNYGFSKLSDLLKAIP 49