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Conserved domains on  [gi|1889613856|ref|WP_182716714|]
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MULTISPECIES: NYN domain-containing protein [Pseudoalteromonas]

Protein Classification

NYN domain-containing protein( domain architecture ID 10180866)

NYN domain-containing protein; the NYN domain shares a common protein fold with PIN (PilT N-terminal)-domain nucleases

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_LabA cd10911
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 13-162 1.76e-47

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; This subfamily contains Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. This subfamily belongs to the LabA-like domain family which includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Also included in the LabA-like domain family are human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB , which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like 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.


:

Pssm-ID: 350235  Cd Length: 154  Bit Score: 151.49  E-value: 1.76e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  13 RVGIFVDVQNIYYTCReSYGKNFDYNAFWRVMQTQYNIECAFAYAIY--RGDEKQNQFQNILRAIGFDVKLKPFIQRRD- 89
Cdd:cd10911     2 RVAVFIDGANLYYAAK-KLGWKIDYEKLLKYLVGGRELVRAYYYTAVddEEDEKQQKFLDALRKIGYEVVTKPLKEFRDe 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1889613856  90 --GSAKGDWDVGITIDMLEQGKNLDKVILLSGDGDFALLLGHLKNQyNVPCDVYGADRLTAEVLKQSAEQFHLID 162
Cdd:cd10911    81 ggGSVKGNVDVEIAVDMLRLADKYDTAILVSGDGDFAPLVEYLQRK-GKRVEVVSFRGSTSKELRRAADRFIDLD 154
 
Name Accession Description Interval E-value
PIN_LabA cd10911
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 13-162 1.76e-47

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; This subfamily contains Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. This subfamily belongs to the LabA-like domain family which includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Also included in the LabA-like domain family are human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB , which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like 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.


Pssm-ID: 350235  Cd Length: 154  Bit Score: 151.49  E-value: 1.76e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  13 RVGIFVDVQNIYYTCReSYGKNFDYNAFWRVMQTQYNIECAFAYAIY--RGDEKQNQFQNILRAIGFDVKLKPFIQRRD- 89
Cdd:cd10911     2 RVAVFIDGANLYYAAK-KLGWKIDYEKLLKYLVGGRELVRAYYYTAVddEEDEKQQKFLDALRKIGYEVVTKPLKEFRDe 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1889613856  90 --GSAKGDWDVGITIDMLEQGKNLDKVILLSGDGDFALLLGHLKNQyNVPCDVYGADRLTAEVLKQSAEQFHLID 162
Cdd:cd10911    81 ggGSVKGNVDVEIAVDMLRLADKYDTAILVSGDGDFAPLVEYLQRK-GKRVEVVSFRGSTSKELRRAADRFIDLD 154
LabA COG1432
NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction ...
 12-163 1.11e-38

NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction only];


Pssm-ID: 441041  Cd Length: 164  Bit Score: 129.25  E-value: 1.11e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  12 PRVGIFVDVQNIYYTCRESyGKNFDYNAFWRVMQTQYNIECAFAYAiYRGDEKQNQFQNILRAIGFDVKLKPFIQRRdGS 91
Cdd:COG1432     1 KRVAVFIDGDNLYAAARDL-GFDIDYEKLLEELAEYGRLVRARAYG-DDTDERQQGFIDALRENGFEVILKPLQQFR-TS 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1889613856  92 AKGDWDVGITIDMLEQ--GKNLDKVILLSGDGDFALLLGHLKnQYNVPCDVYGADRLTAEVLKQSAEQFHLIDN 163
Cdd:COG1432    78 GKNAVDVELAVDAMELayTPNIDTFVLVSGDSDFTPLVERLR-ERGKRVEVVGVEGKTSDALRNAADEFIDLDD 150
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 13-159 1.07e-32

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.


Pssm-ID: 426520  Cd Length: 137  Bit Score: 113.15  E-value: 1.07e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  13 RVGIFVDVQNIyytcreSYGKNFDYNAFWRVMQTQYNIECAFAYAIyRGDEKQNQFQNILRAIGFDVKLKPFIQrrdgsA 92
Cdd:pfam01936   1 RVAVFIDGENC------PLPDGVDYRKVLEEIRSGGEVVRARAYGN-WGDPDLRKFPDALSSTGIPVQHKPLTK-----G 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  93 KGDWDVGITIDMLEQG--KNLDKVILLSGDGDFALLLGHLKNqYNVPCDVYGA-DRLTAEVLKQSAEQFH 159
Cdd:pfam01936  69 KNAVDVGLAVDALELAydNNPDTFVLVSGDGDFAPLLERLRE-RGKRVEVLGAeEPSTSDALINAADRFI 137
 
Name Accession Description Interval E-value
PIN_LabA cd10911
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 13-162 1.76e-47

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; This subfamily contains Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. This subfamily belongs to the LabA-like domain family which includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Also included in the LabA-like domain family are human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB , which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like 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.


Pssm-ID: 350235  Cd Length: 154  Bit Score: 151.49  E-value: 1.76e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  13 RVGIFVDVQNIYYTCReSYGKNFDYNAFWRVMQTQYNIECAFAYAIY--RGDEKQNQFQNILRAIGFDVKLKPFIQRRD- 89
Cdd:cd10911     2 RVAVFIDGANLYYAAK-KLGWKIDYEKLLKYLVGGRELVRAYYYTAVddEEDEKQQKFLDALRKIGYEVVTKPLKEFRDe 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1889613856  90 --GSAKGDWDVGITIDMLEQGKNLDKVILLSGDGDFALLLGHLKNQyNVPCDVYGADRLTAEVLKQSAEQFHLID 162
Cdd:cd10911    81 ggGSVKGNVDVEIAVDMLRLADKYDTAILVSGDGDFAPLVEYLQRK-GKRVEVVSFRGSTSKELRRAADRFIDLD 154
LabA COG1432
NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction ...
 12-163 1.11e-38

NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction only];


Pssm-ID: 441041  Cd Length: 164  Bit Score: 129.25  E-value: 1.11e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  12 PRVGIFVDVQNIYYTCRESyGKNFDYNAFWRVMQTQYNIECAFAYAiYRGDEKQNQFQNILRAIGFDVKLKPFIQRRdGS 91
Cdd:COG1432     1 KRVAVFIDGDNLYAAARDL-GFDIDYEKLLEELAEYGRLVRARAYG-DDTDERQQGFIDALRENGFEVILKPLQQFR-TS 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1889613856  92 AKGDWDVGITIDMLEQ--GKNLDKVILLSGDGDFALLLGHLKnQYNVPCDVYGADRLTAEVLKQSAEQFHLIDN 163
Cdd:COG1432    78 GKNAVDVELAVDAMELayTPNIDTFVLVSGDSDFTPLVERLR-ERGKRVEVVGVEGKTSDALRNAADEFIDLDD 150
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 13-159 1.07e-32

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.


Pssm-ID: 426520  Cd Length: 137  Bit Score: 113.15  E-value: 1.07e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  13 RVGIFVDVQNIyytcreSYGKNFDYNAFWRVMQTQYNIECAFAYAIyRGDEKQNQFQNILRAIGFDVKLKPFIQrrdgsA 92
Cdd:pfam01936   1 RVAVFIDGENC------PLPDGVDYRKVLEEIRSGGEVVRARAYGN-WGDPDLRKFPDALSSTGIPVQHKPLTK-----G 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  93 KGDWDVGITIDMLEQG--KNLDKVILLSGDGDFALLLGHLKNqYNVPCDVYGA-DRLTAEVLKQSAEQFH 159
Cdd:pfam01936  69 KNAVDVGLAVDALELAydNNPDTFVLVSGDGDFAPLLERLRE-RGKRVEVLGAeEPSTSDALINAADRFI 137
PIN_SF cd09852
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
 18-131 7.70e-09

PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. 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. The PIN domain superfamily includes: the FEN-like PIN domain family such as the PIN domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. It also includes the Mut7-C PIN domain family, which is not represented here as it is a shortened version of the PIN fold and lacks a core strand and helix (H3 and S3). The Mut7-C PIN domain family includes the C-terminus of Caenorhabditis elegans exonuclease Mut-7.


Pssm-ID: 350203  Cd Length: 114  Bit Score: 51.09  E-value: 7.70e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  18 VDVQNIYYTCRES---YGKNFDYNAFWRVMQTQYN---IECAFAYAIYRGDEKQNQFQNILRAIGFDVKLKPFIqrrdgs 91
Cdd:cd09852     2 VDGSNMIYTCREAvrtYRLNFDMAQRQYVAKEGVSpivVFDASPVQLKVKVTKNDRKQLQFHGVGFAV*LTPPI------ 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1889613856  92 akGDWDVGITIDMLEqgknLDKVILLSGDGDFALLLGHLK 131
Cdd:cd09852    76 --SDADVGIAALAIA----IDRVALATGDGDFLAIVENKG 109
PIN_NicB-like cd18722
LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from ...
 13-136 5.84e-07

LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from Pseudomonas putida S16 is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine. This subfamily also includes the uncharacterized CPP15 (plasmid) protein from Campylobacter jejuni. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. 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.


Pssm-ID: 350289  Cd Length: 117  Bit Score: 46.01  E-value: 5.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  13 RVGIFVDVQNIYYTCRESYGKNFdYNAFWrvmqtqYNIECAFAyAIYRGDEKQNQFQNIlraigfdvklKPFIQRRDGSA 92
Cdd:cd18722     1 RTAVYVDGFNLYYGLKAREELKL-YRYYW------LDLPPLAK-NLLLPDPSQELLERV----------KYFTARVNSSP 62

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1889613856  93 ---KGDwDVGITIDMLE--QGKNLDKVILLSGDGDFALLLGHLKNQYNV 136
Cdd:cd18722    63 keeKGV-DVNIALDILSdaYKKQVDQAVLVSGDSDFVPAVKLARREPGI 110
PIN_LabA-like cd06167
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 15-143 5.81e-06

PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression. This family also includes the N-terminal domain of limkain b1, a human autoantigen associated with cytoplasmic vesicles. Other members are the LabA-like PIN domains of human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. 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 this family.


Pssm-ID: 350201  Cd Length: 113  Bit Score: 43.17  E-value: 5.81e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1889613856  15 GIFVDVQNIYYTCResygkNFDYNAFWRVMQTQYNIecafAYAIYRGDEKQNQFQNILraiGFDVKLKPFIQrrdgsaKG 94
Cdd:cd06167     1 GVLVDADNCSNGFG-----ALILRRYAGLFLQMGFE----KYANINAQPLLVPPSNNR---GFTVIRVAAKR------KD 62

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1889613856  95 DWDVGITID---MLEQGKNlDKVILLSGDG-DFALLLgHLKNQYNVPCDVYGA 143
Cdd:cd06167    63 AADVALVRQagrLAYTGAP-DTVVLVSGDKlDFSDLI-EKAKEAGLNVIVVGP 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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