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Conserved domains on  [gi|489516364|ref|WP_003421194|]
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NYN domain-containing protein [Clostridioides difficile]

Protein Classification

NYN domain-containing protein( domain architecture ID 10532326)

NYN domain-containing protein may function as a nuclease; 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
NYN_YacP pfam05991
YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family ...
 9-173 6.81e-73

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: 216.66  E-value: 6.81e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364    9 LIIDGYNIINAWDNLKELA-KEDLEDSREKLIDDIIEFSEFMGYKTIIVFDAYNVKNSREKVEKRKHITIVYTREHQTAD 87
Cdd:pfam05991   1 LLVDGYNVIGAWPELKELKdRGDLEAARDKLIEILANYQAYTGYEVIVVFDAHYVPGPEEKEEKYGGIEVVYTKEGETAD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364   88 SYIEKFITSLSKYDDVKVATNDYAEQQMILGKGATRMSARELKLELDRSKNKMKEKNIGlRKKIQRNWLEERLDKETLSK 167
Cdd:pfam05991  81 SYIERLVAELGRKTRVTVATSDRAEQQTIFGQGALRLSARELYEEVEAAEKKIKKKVEK-RKEKRRNYLEDRLSPEVLEK 159


                  ....*.
gi 489516364  168 LENIRR 173
Cdd:pfam05991 160 LEKLRR 165
 
Name Accession Description Interval E-value
NYN_YacP pfam05991
YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family ...
 9-173 6.81e-73

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: 216.66  E-value: 6.81e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364    9 LIIDGYNIINAWDNLKELA-KEDLEDSREKLIDDIIEFSEFMGYKTIIVFDAYNVKNSREKVEKRKHITIVYTREHQTAD 87
Cdd:pfam05991   1 LLVDGYNVIGAWPELKELKdRGDLEAARDKLIEILANYQAYTGYEVIVVFDAHYVPGPEEKEEKYGGIEVVYTKEGETAD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364   88 SYIEKFITSLSKYDDVKVATNDYAEQQMILGKGATRMSARELKLELDRSKNKMKEKNIGlRKKIQRNWLEERLDKETLSK 167
Cdd:pfam05991  81 SYIERLVAELGRKTRVTVATSDRAEQQTIFGQGALRLSARELYEEVEAAEKKIKKKVEK-RKEKRRNYLEDRLSPEVLEK 159


                  ....*.
gi 489516364  168 LENIRR 173
Cdd:pfam05991 160 LEKLRR 165
Rae1 COG3688
EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN ...
 7-175 9.52e-72

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: 213.57  E-value: 9.52e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364   7 HYLIIDGYNIINAWDNLKELAKEDLEDSREKLIDDIIEFSEFMGYKTIIVFDAYNVKNSREKVEKRKHITIVYTREHQTA 86
Cdd:COG3688    1 EILLVDGYNVIGAWPELKELKDDSLEAARDKLIEILANYAAFTGYEVIVVFDAHYVPGSEEKEEKYGGVEVVFTKEGETA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364  87 DSYIEKFITSLS-KYDDVKVATNDYAEQQMILGKGATRMSARELKLELDRSKNKMKEKniGLRKKIQRNWLEERLDKETL 165
Cdd:COG3688   81 DSYIERLVAELRnRPRRVTVVTSDRAEQRTVFGRGALRISARELLREVEEAKREIRKK--IKKKKPKRNTLKDRLDPEVL 158

                        170
                 ....*....|
gi 489516364 166 SKLENIRRKR 175
Cdd:COG3688  159 EKLEKLRRGK 168
PIN_YacP-like cd10912
PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also ...
 8-143 2.33e-59

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: 181.22  E-value: 2.33e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364   8 YLIIDGYNIINAWDNLKELAKEDLEDSREKLIDDIIEFSEFMGYKTIIVFDAYNVKNSREKVEKRKHITIVYTREHQTAD 87
Cdd:cd10912    1 ILLVDGYNVIGAWPELKKLKRESLEEARDKLIEELANYQAYKGYEVIVVFDAYYVKGGLEKEEESGGVEVVFTKEGETAD 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489516364  88 SYIEKFITSL-SKYDDVKVATNDYAEQQMILGKGATRMSARELKLELDRSKNKMKEK 143
Cdd:cd10912   81 SYIERLVASLkRRCKRVTVATSDRAEQRTVFGQGALRISARELLKEIERAKEEIRRS 137
 
Name Accession Description Interval E-value
NYN_YacP pfam05991
YacP-like NYN domain; This family consists of bacterial proteins related to YacP. This family ...
 9-173 6.81e-73

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: 216.66  E-value: 6.81e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364    9 LIIDGYNIINAWDNLKELA-KEDLEDSREKLIDDIIEFSEFMGYKTIIVFDAYNVKNSREKVEKRKHITIVYTREHQTAD 87
Cdd:pfam05991   1 LLVDGYNVIGAWPELKELKdRGDLEAARDKLIEILANYQAYTGYEVIVVFDAHYVPGPEEKEEKYGGIEVVYTKEGETAD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364   88 SYIEKFITSLSKYDDVKVATNDYAEQQMILGKGATRMSARELKLELDRSKNKMKEKNIGlRKKIQRNWLEERLDKETLSK 167
Cdd:pfam05991  81 SYIERLVAELGRKTRVTVATSDRAEQQTIFGQGALRLSARELYEEVEAAEKKIKKKVEK-RKEKRRNYLEDRLSPEVLEK 159


                  ....*.
gi 489516364  168 LENIRR 173
Cdd:pfam05991 160 LEKLRR 165
Rae1 COG3688
EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN ...
 7-175 9.52e-72

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: 213.57  E-value: 9.52e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364   7 HYLIIDGYNIINAWDNLKELAKEDLEDSREKLIDDIIEFSEFMGYKTIIVFDAYNVKNSREKVEKRKHITIVYTREHQTA 86
Cdd:COG3688    1 EILLVDGYNVIGAWPELKELKDDSLEAARDKLIEILANYAAFTGYEVIVVFDAHYVPGSEEKEEKYGGVEVVFTKEGETA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364  87 DSYIEKFITSLS-KYDDVKVATNDYAEQQMILGKGATRMSARELKLELDRSKNKMKEKniGLRKKIQRNWLEERLDKETL 165
Cdd:COG3688   81 DSYIERLVAELRnRPRRVTVVTSDRAEQRTVFGRGALRISARELLREVEEAKREIRKK--IKKKKPKRNTLKDRLDPEVL 158

                        170
                 ....*....|
gi 489516364 166 SKLENIRRKR 175
Cdd:COG3688  159 EKLEKLRRGK 168
PIN_YacP-like cd10912
PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins; Bacillus subtilis YacP, also ...
 8-143 2.33e-59

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: 181.22  E-value: 2.33e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364   8 YLIIDGYNIINAWDNLKELAKEDLEDSREKLIDDIIEFSEFMGYKTIIVFDAYNVKNSREKVEKRKHITIVYTREHQTAD 87
Cdd:cd10912    1 ILLVDGYNVIGAWPELKKLKRESLEEARDKLIEELANYQAYKGYEVIVVFDAYYVKGGLEKEEESGGVEVVFTKEGETAD 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 489516364  88 SYIEKFITSL-SKYDDVKVATNDYAEQQMILGKGATRMSARELKLELDRSKNKMKEK 143
Cdd:cd10912   81 SYIERLVASLkRRCKRVTVATSDRAEQRTVFGQGALRISARELLKEIERAKEEIRRS 137
PIN_SF cd09852
PIN (PilT N terminus) domain: Superfamily; The PIN (PilT N terminus) domain belongs to a large ...
 10-125 8.48e-03

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: 34.52  E-value: 8.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489516364  10 IIDGYNIINAWDNLKelakedledSREKLIDDIIEFSEFM--GYKTIIVFDAYNV-------KNSREKVEKRKH-ITIVY 79
Cdd:cd09852    1 LVDGSNMIYTCREAV---------RTYRLNFDMAQRQYVAkeGVSPIVVFDASPVqlkvkvtKNDRKQLQFHGVgFAV*L 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 489516364  80 TREHQTADSYIEKFITSLSKYddvKVATNDYAEQQMILGKGATRMS 125
Cdd:cd09852   72 TPPISDADVGIAALAIAIDRV---ALATGDGDFLAIVENKGVTVYR 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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