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Conserved domains on  [gi|334184108|ref|NP_001189500|]
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yacP-like NYN domain protein [Arabidopsis thaliana]

Protein Classification

NYN domain-containing protein( domain architecture ID 12971081)

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_YacP-like cd10912
PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also ...
 84-225 8.72e-48

PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also known as Rae1, is an endoribonuclease involved in ribosome-dependent mRNA decay. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. PIN domains 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 putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


:

Pssm-ID: 350236  Cd Length: 142  Bit Score: 155.03  E-value: 8.72e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108  84 VLLVDGYNVCGYWMKLKKHFmKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMSGLPTHKEDF-AGVDVIFSGE-TCA 161
Cdd:cd10912    1 ILLVDGYNVIGAWPELKKLK-RESLEEARDKLIEELANYQAYKGYEVIVVFDAYYVKGGLEKEEEsGGVEVVFTKEgETA 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334184108 162 DAWIEKEVVALREDgCPKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEIKSMHKEVEKMMQETR 225
Cdd:cd10912   80 DSYIERLVASLKRR-CKRVTVATSDRAEQRTVFGQGALRISARELLKEIERAKEEIRRSKRRTK 142
 
Name Accession Description Interval E-value
PIN_YacP-like cd10912
PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also ...
 84-225 8.72e-48

PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also known as Rae1, is an endoribonuclease involved in ribosome-dependent mRNA decay. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. PIN domains 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 putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350236  Cd Length: 142  Bit Score: 155.03  E-value: 8.72e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108  84 VLLVDGYNVCGYWMKLKKHFmKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMSGLPTHKEDF-AGVDVIFSGE-TCA 161
Cdd:cd10912    1 ILLVDGYNVIGAWPELKKLK-RESLEEARDKLIEELANYQAYKGYEVIVVFDAYYVKGGLEKEEEsGGVEVVFTKEgETA 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334184108 162 DAWIEKEVVALREDgCPKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEIKSMHKEVEKMMQETR 225
Cdd:cd10912   80 DSYIERLVASLKRR-CKRVTVATSDRAEQRTVFGQGALRISARELLKEIERAKEEIRRSKRRTK 142
NYN_YacP pfam05991
YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family ...
 85-251 9.07e-47

YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family is uncharacterized functionally, but it has been suggested that these proteins are nucleases due to them containing a NYN domain. NYN (for N4BP1, YacP-like Nuclease) domains were discovered by Anantharaman and Aravind. Based on gene neighborhoods it was suggested that the bacterial YacP proteins interact with the Ribonuclease III and TrmH methylase in a processome complex that catalyzes the maturation of rRNA and tRNA.


Pssm-ID: 428711  Cd Length: 165  Bit Score: 153.49  E-value: 9.07e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108   85 LLVDGYNVCGYWMKLKKHFMKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMS-GLPTHKEDFAGVDVIFS--GETcA 161
Cdd:pfam05991   1 LLVDGYNVIGAWPELKELKDRGDLEAARDKLIEILANYQAYTGYEVIVVFDAHYVpGPEEKEEKYGGIEVVYTkeGET-A 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108  162 DAWIEKEVVALREDGcpKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEIKSMHKEVEKMMQETRSTsfQGRLLKHNLDSE 241
Cdd:pfam05991  80 DSYIERLVAELGRKT--RVTVATSDRAEQQTIFGQGALRLSARELYEEVEAAEKKIKKKVEKRKEK--RRNYLEDRLSPE 155

                         170
                  ....*....|
gi 334184108  242 VVDALKDLRD 251
Cdd:pfam05991 156 VLEKLEKLRR 165
Rae1 COG3688
EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN ...
 84-253 3.78e-34

EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442904  Cd Length: 168  Bit Score: 121.12  E-value: 3.78e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108  84 VLLVDGYNVCGYWMKLKKhFMKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMS-GLPTHKEDFAGVDVIFS--GETc 160
Cdd:COG3688    2 ILLVDGYNVIGAWPELKE-LKDDSLEAARDKLIEILANYAAFTGYEVIVVFDAHYVpGSEEKEEKYGGVEVVFTkeGET- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108 161 ADAWIEKEVVALREDGCpKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEIKSMHKEVEKMMQETRStsfQGRLLKHNLDS 240
Cdd:COG3688   80 ADSYIERLVAELRNRPR-RVTVVTSDRAEQRTVFGRGALRISARELLREVEEAKREIRKKIKKKKP---KRNTLKDRLDP 155

                        170
                 ....*....|...
gi 334184108 241 EVVDALKDLRDKL 253
Cdd:COG3688  156 EVLEKLEKLRRGK 168
 
Name Accession Description Interval E-value
PIN_YacP-like cd10912
PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also ...
 84-225 8.72e-48

PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also known as Rae1, is an endoribonuclease involved in ribosome-dependent mRNA decay. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. PIN domains 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 putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons.


Pssm-ID: 350236  Cd Length: 142  Bit Score: 155.03  E-value: 8.72e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108  84 VLLVDGYNVCGYWMKLKKHFmKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMSGLPTHKEDF-AGVDVIFSGE-TCA 161
Cdd:cd10912    1 ILLVDGYNVIGAWPELKKLK-RESLEEARDKLIEELANYQAYKGYEVIVVFDAYYVKGGLEKEEEsGGVEVVFTKEgETA 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 334184108 162 DAWIEKEVVALREDgCPKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEIKSMHKEVEKMMQETR 225
Cdd:cd10912   80 DSYIERLVASLKRR-CKRVTVATSDRAEQRTVFGQGALRISARELLKEIERAKEEIRRSKRRTK 142
NYN_YacP pfam05991
YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family ...
 85-251 9.07e-47

YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family is uncharacterized functionally, but it has been suggested that these proteins are nucleases due to them containing a NYN domain. NYN (for N4BP1, YacP-like Nuclease) domains were discovered by Anantharaman and Aravind. Based on gene neighborhoods it was suggested that the bacterial YacP proteins interact with the Ribonuclease III and TrmH methylase in a processome complex that catalyzes the maturation of rRNA and tRNA.


Pssm-ID: 428711  Cd Length: 165  Bit Score: 153.49  E-value: 9.07e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108   85 LLVDGYNVCGYWMKLKKHFMKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMS-GLPTHKEDFAGVDVIFS--GETcA 161
Cdd:pfam05991   1 LLVDGYNVIGAWPELKELKDRGDLEAARDKLIEILANYQAYTGYEVIVVFDAHYVpGPEEKEEKYGGIEVVYTkeGET-A 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108  162 DAWIEKEVVALREDGcpKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEIKSMHKEVEKMMQETRSTsfQGRLLKHNLDSE 241
Cdd:pfam05991  80 DSYIERLVAELGRKT--RVTVATSDRAEQQTIFGQGALRLSARELYEEVEAAEKKIKKKVEKRKEK--RRNYLEDRLSPE 155

                         170
                  ....*....|
gi 334184108  242 VVDALKDLRD 251
Cdd:pfam05991 156 VLEKLEKLRR 165
Rae1 COG3688
EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN ...
 84-253 3.78e-34

EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442904  Cd Length: 168  Bit Score: 121.12  E-value: 3.78e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108  84 VLLVDGYNVCGYWMKLKKhFMKGRLDVARQKLVDELVSFSMVKEVKVVVVFDALMS-GLPTHKEDFAGVDVIFS--GETc 160
Cdd:COG3688    2 ILLVDGYNVIGAWPELKE-LKDDSLEAARDKLIEILANYAAFTGYEVIVVFDAHYVpGSEEKEEKYGGVEVVFTkeGET- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 334184108 161 ADAWIEKEVVALREDGCpKVWVVTSDVCQQQAAHGAGAYIWSSKALVSEIKSMHKEVEKMMQETRStsfQGRLLKHNLDS 240
Cdd:COG3688   80 ADSYIERLVAELRNRPR-RVTVVTSDRAEQRTVFGRGALRISARELLREVEEAKREIRKKIKKKKP---KRNTLKDRLDP 155

                        170
                 ....*....|...
gi 334184108 241 EVVDALKDLRDKL 253
Cdd:COG3688  156 EVLEKLEKLRRGK 168
 
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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