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Conserved domains on  [gi|491622711|ref|WP_005480252|]
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MULTISPECIES: NYN domain-containing protein [Vibrio]

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; ...
 7-157 1.65e-49

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: 156.11  E-value: 1.65e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711   7 EKIAILVDVQNVYYTCREaYRSNFDYNQFWYVATQEKEVVSAKAYAI--ASNDPKQRQFHHILRGVGFEVMLKPYIQRRD 84
Cdd:cd10911    1 ERVAVFIDGANLYYAAKK-LGWKIDYEKLLKYLVGGRELVRAYYYTAvdDEEDEKQQKFLDALRKIGYEVVTKPLKEFRD 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491622711  85 ---GSAKGDWDVGITLDAIEIAPDVDRVILVSGDGDFSLLVERIQQRyNKKVTVYGVPRLTSQTLIDCADNFVAID 157
Cdd:cd10911   80 eggGSVKGNVDVEIAVDMLRLADKYDTAILVSGDGDFAPLVEYLQRK-GKRVEVVSFRGSTSKELRRAADRFIDLD 154
 
Name Accession Description Interval E-value
PIN_LabA cd10911
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 7-157 1.65e-49

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: 156.11  E-value: 1.65e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711   7 EKIAILVDVQNVYYTCREaYRSNFDYNQFWYVATQEKEVVSAKAYAI--ASNDPKQRQFHHILRGVGFEVMLKPYIQRRD 84
Cdd:cd10911    1 ERVAVFIDGANLYYAAKK-LGWKIDYEKLLKYLVGGRELVRAYYYTAvdDEEDEKQQKFLDALRKIGYEVVTKPLKEFRD 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491622711  85 ---GSAKGDWDVGITLDAIEIAPDVDRVILVSGDGDFSLLVERIQQRyNKKVTVYGVPRLTSQTLIDCADNFVAID 157
Cdd:cd10911   80 eggGSVKGNVDVEIAVDMLRLADKYDTAILVSGDGDFAPLVEYLQRK-GKRVEVVSFRGSTSKELRRAADRFIDLD 154
LabA COG1432
NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction ...
 7-158 2.23e-47

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


Pssm-ID: 441041  Cd Length: 164  Bit Score: 151.20  E-value: 2.23e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711   7 EKIAILVDVQNVYYTCREAYRsNFDYNQFWYVATQEKEVVSAKAYAiASNDPKQRQFHHILRGVGFEVMLKPYIQRRdGS 86
Cdd:COG1432    1 KRVAVFIDGDNLYAAARDLGF-DIDYEKLLEELAEYGRLVRARAYG-DDTDERQQGFIDALRENGFEVILKPLQQFR-TS 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491622711  87 AKGDWDVGITLDAIEIA--PDVDRVILVSGDGDFSLLVERIQQRyNKKVTVYGVPRLTSQTLIDCADNFVAIDD 158
Cdd:COG1432   78 GKNAVDVELAVDAMELAytPNIDTFVLVSGDSDFTPLVERLRER-GKRVEVVGVEGKTSDALRNAADEFIDLDD 150
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 8-154 1.39e-33

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: 115.46  E-value: 1.39e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711    8 KIAILVDVQNVyytcreAYRSNFDYNQFWYVATQEKEVVSAKAYAIASnDPKQRQFHHILRGVGFEVMLKPYIQrrdgsA 87
Cdd:pfam01936   1 RVAVFIDGENC------PLPDGVDYRKVLEEIRSGGEVVRARAYGNWG-DPDLRKFPDALSSTGIPVQHKPLTK-----G 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711   88 KGDWDVGITLDAIEIA--PDVDRVILVSGDGDFSLLVERIqQRYNKKVTVYGVPR-LTSQTLIDCADNFV 154
Cdd:pfam01936  69 KNAVDVGLAVDALELAydNNPDTFVLVSGDGDFAPLLERL-RERGKRVEVLGAEEpSTSDALINAADRFI 137
 
Name Accession Description Interval E-value
PIN_LabA cd10911
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 7-157 1.65e-49

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: 156.11  E-value: 1.65e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711   7 EKIAILVDVQNVYYTCREaYRSNFDYNQFWYVATQEKEVVSAKAYAI--ASNDPKQRQFHHILRGVGFEVMLKPYIQRRD 84
Cdd:cd10911    1 ERVAVFIDGANLYYAAKK-LGWKIDYEKLLKYLVGGRELVRAYYYTAvdDEEDEKQQKFLDALRKIGYEVVTKPLKEFRD 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491622711  85 ---GSAKGDWDVGITLDAIEIAPDVDRVILVSGDGDFSLLVERIQQRyNKKVTVYGVPRLTSQTLIDCADNFVAID 157
Cdd:cd10911   80 eggGSVKGNVDVEIAVDMLRLADKYDTAILVSGDGDFAPLVEYLQRK-GKRVEVVSFRGSTSKELRRAADRFIDLD 154
LabA COG1432
NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction ...
 7-158 2.23e-47

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


Pssm-ID: 441041  Cd Length: 164  Bit Score: 151.20  E-value: 2.23e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711   7 EKIAILVDVQNVYYTCREAYRsNFDYNQFWYVATQEKEVVSAKAYAiASNDPKQRQFHHILRGVGFEVMLKPYIQRRdGS 86
Cdd:COG1432    1 KRVAVFIDGDNLYAAARDLGF-DIDYEKLLEELAEYGRLVRARAYG-DDTDERQQGFIDALRENGFEVILKPLQQFR-TS 77

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491622711  87 AKGDWDVGITLDAIEIA--PDVDRVILVSGDGDFSLLVERIQQRyNKKVTVYGVPRLTSQTLIDCADNFVAIDD 158
Cdd:COG1432   78 GKNAVDVELAVDAMELAytPNIDTFVLVSGDSDFTPLVERLRER-GKRVEVVGVEGKTSDALRNAADEFIDLDD 150
NYN pfam01936
NYN domain; These domains are found in the eukaryotic proteins typified by the Nedd4-binding ...
 8-154 1.39e-33

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: 115.46  E-value: 1.39e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711    8 KIAILVDVQNVyytcreAYRSNFDYNQFWYVATQEKEVVSAKAYAIASnDPKQRQFHHILRGVGFEVMLKPYIQrrdgsA 87
Cdd:pfam01936   1 RVAVFIDGENC------PLPDGVDYRKVLEEIRSGGEVVRARAYGNWG-DPDLRKFPDALSSTGIPVQHKPLTK-----G 68

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711   88 KGDWDVGITLDAIEIA--PDVDRVILVSGDGDFSLLVERIqQRYNKKVTVYGVPR-LTSQTLIDCADNFV 154
Cdd:pfam01936  69 KNAVDVGLAVDALELAydNNPDTFVLVSGDGDFAPLLERL-RERGKRVEVLGAEEpSTSDALINAADRFI 137
PIN_SF cd09852
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
 12-137 3.22e-21

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: 83.06  E-value: 3.22e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711  12 LVDVQNVYYTCREA---YRSNFDYNQFWYVAtqeKEVVSAKAYAIAS----------NDPKQRQFHhilrGVGFEVMLKP 78
Cdd:cd09852    1 LVDGSNMIYTCREAvrtYRLNFDMAQRQYVA---KEGVSPIVVFDASpvqlkvkvtkNDRKQLQFH----GVGFAV*LTP 73

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 491622711  79 YIqrrdgsakGDWDVGITLDAIEIapdvDRVILVSGDGDFSLLVEriqqryNKKVTVYG 137
Cdd:cd09852   74 PI--------SDADVGIAALAIAI----DRVALATGDGDFLAIVE------NKGVTVYR 114
PIN_LabA-like cd06167
PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins; ...
 10-138 3.36e-17

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: 72.45  E-value: 3.36e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711  10 AILVDVQNVYYTCReayrsNFDYNQFWYVATQekevVSAKAYA-IASNDPKQRQFHhilrGVGFEVMLKPYIQrrdgsaK 88
Cdd:cd06167    1 GVLVDADNCSNGFG-----ALILRRYAGLFLQ----MGFEKYAnINAQPLLVPPSN----NRGFTVIRVAAKR------K 61

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 491622711  89 GDWDVGITLDAIEIAPD--VDRVILVSGDG-DFSLLVERIqQRYNKKVTVYGV 138
Cdd:cd06167   62 DAADVALVRQAGRLAYTgaPDTVVLVSGDKlDFSDLIEKA-KEAGLNVIVVGP 113
PIN_LabA-like_N_1 cd11297
uncharacterized subfamily of N-terminal LabA-like PIN domains; This N-terminal LabA-like PIN ...
 9-138 1.84e-10

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.


Pssm-ID: 350237  Cd Length: 117  Bit Score: 55.16  E-value: 1.84e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711   9 IAILVDVQNVYYTCREAyrsNFDYnqfwyvATQEKEVVSAKAYAIASNdPKQRQFHHILRGVGFE-VMLKPYIQRRDGSa 87
Cdd:cd11297    1 IAVLIDAENISASYADA---ILEE------LAKYGRVVVRRAYGDWSS-PRLKGWKDELLEHGIEpIQQFSYTKGKNAA- 69

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 491622711  88 kgdwDVGITLDAIEIA--PDVDRVILVSGDGDFSLLVERIQQrYNKKVTVYGV 138
Cdd:cd11297   70 ----DIALVIDAMDLLytGRIDTFVIVSSDSDFTPLAQRLRE-LGKTVIGIGE 117
PIN_NicB-like cd18722
LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins; Curiously NicB from ...
 8-135 3.84e-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: 46.40  E-value: 3.84e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491622711   8 KIAILVDVQNVYYTCREAYRSNFdYNQFWYVAtqekevvsakayaiasnDPKQRQFHHILRGVGFEVMLKPYIQRRDGSA 87
Cdd:cd18722    1 RTAVYVDGFNLYYGLKAREELKL-YRYYWLDL-----------------PPLAKNLLLPDPSQELLERVKYFTARVNSSP 62

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 491622711  88 ---KGDwDVGITLDAIEIA--PDVDRVILVSGDGDFSLLVERIQQRYNKKVTV 135
Cdd:cd18722   63 keeKGV-DVNIALDILSDAykKQVDQAVLVSGDSDFVPAVKLARREPGIRVGL 114
 
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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