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Conserved domains on  [gi|785769726|gb|AJZ75644|]
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nucleotide-binding protein [Candidatus Nitrosotenuis cloacae]

Protein Classification

NOB1 family endonuclease( domain architecture ID 11444510)

NOB1 (nin one binding) family endonuclease similar to Archaeoglobus fulgidus endonuclease Nob1 (also known as type II toxin-antitoxin system VapC8 toxin) which cleaves pre-16S-rRNA at the D-site to yield the mature 3' end

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Nob1 COG1439
rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis];
1-158 1.53e-68

rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis];


:

Pssm-ID: 441048 [Multi-domain]  Cd Length: 155  Bit Score: 204.70  E-value: 1.53e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726   1 MASRVYDASAFYAGIPFasPEIGLTTTVIFEEIKHIKQRHgALDtLLDTDRLRIKDPLKSSIDVVMNAAKKTGDAQKLSK 80
Cdd:COG1439    1 MMMYVLDASAFIAGYPL--DGELYTTPSVIEELKDIKSRL-RLE-ALEGGGLRIREPDPESIEKVKKAARKTGDLEELSK 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 785769726  81 ADISAVALAHEIKGNLVTDDFAVSNLAKNLGLQVNPIMTKGIKDVGHWIHYCVGCSKEFS-GLEFCPNCGNKLSRRLLK 158
Cdd:COG1439   77 TDISVLALALELDATLVTDDYALQNVAKHLGIKVEPIATKGIKEVRKWRYRCTGCGREFDePEEECPICGSPLKRKRKK 155
 
Name Accession Description Interval E-value
Nob1 COG1439
rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis];
1-158 1.53e-68

rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441048 [Multi-domain]  Cd Length: 155  Bit Score: 204.70  E-value: 1.53e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726   1 MASRVYDASAFYAGIPFasPEIGLTTTVIFEEIKHIKQRHgALDtLLDTDRLRIKDPLKSSIDVVMNAAKKTGDAQKLSK 80
Cdd:COG1439    1 MMMYVLDASAFIAGYPL--DGELYTTPSVIEELKDIKSRL-RLE-ALEGGGLRIREPDPESIEKVKKAARKTGDLEELSK 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 785769726  81 ADISAVALAHEIKGNLVTDDFAVSNLAKNLGLQVNPIMTKGIKDVGHWIHYCVGCSKEFS-GLEFCPNCGNKLSRRLLK 158
Cdd:COG1439   77 TDISVLALALELDATLVTDDYALQNVAKHLGIKVEPIATKGIKEVRKWRYRCTGCGREFDePEEECPICGSPLKRKRKK 155
PRK12496 PRK12496
hypothetical protein; Provisional
 4-161 1.59e-40

hypothetical protein; Provisional


Pssm-ID: 237118 [Multi-domain]  Cd Length: 164  Bit Score: 133.98  E-value: 1.59e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726   4 RVYDASAFYAGIPFASPEiGLTTTVIFEEIKHIKQRHgALDTLLDTDRLRIKDPLKSSIDVVMNAAKKTGDAQKLSKADI 83
Cdd:PRK12496   4 KVLDASAFIHGYNPEDGE-HYTTPSVVEEVKDKESRL-ILESAISAGKLKILEPSPESIEKVEEAAIKTGDLMRLSNTDI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726  84 SAVALAHEIKGNLVTDDFAVSNLAKNLGLQVNPIMTKGIKDVGHWIHYCVGCSKEFSGL---EFCPNCGNKLSRRLLKGK 160
Cdd:PRK12496  82 EVLALALELNGTLYTDDYGIQNVAKKLNIKFENIKTKGIKKVIKWRKVCKGCKKKYPEDypdDVCEICGSPVKRKMVKRR 161


                 .
gi 785769726 161 S 161
Cdd:PRK12496 162 L 162
PIN_Nob1-like cd09876
VapC-like PIN domain of eukaryotic ribosome assembly factor Nob1 and archaeal UPF0129 protein ...
 5-117 2.30e-33

VapC-like PIN domain of eukaryotic ribosome assembly factor Nob1 and archaeal UPF0129 protein Ta0041-like homologs; PIN (PilT N terminus) domain of the Saccharomyces cerevisiae ribosome assembly factor, Nob1 (Nin one binding) protein, the Thermoplasma acidophilum DSM 1728, UPF0129 protein Ta0041, and similar eukaryotic and archaeal homologs are included in this family. The Nob1 PIN domain binds the single-stranded cleavage site D at the 3-prime end of 18S rRNA. Recombinant Nob1 binds as a tetramer to pre-18S rRNA fragments containing cleavage site D and believed to cleave at this site. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. 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. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_6.


Pssm-ID: 350224  Cd Length: 112  Bit Score: 113.76  E-value: 2.30e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726   5 VYDASAFYAGIPFASPEIGL-TTTVIFEEIKHIKQRHgALDTLLDtdRLRIKDPLKSSIDVVMNAAKKTGDAQKLSKADI 83
Cdd:cd09876    2 VLDTSAFISGAPLDGLAEKLyTTPEVLEEIRDKKSRL-RLELLPG--KLKVREPSEESIKAVKEFAKKTGDYGSLSATDI 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 785769726  84 SAVALAHEIKGNLVTDDFAVSNLAKNLGLQVNPI 117
Cdd:cd09876   79 KVLALALELEAEIVTDDYAIQNVAKHLGIKFKSI 112
PIN_6 pfam17146
PIN domain of ribonuclease; This is a PIN domain found in eukaryotic ribonuclease Nob1 and ...
 5-92 1.51e-14

PIN domain of ribonuclease; This is a PIN domain found in eukaryotic ribonuclease Nob1 and archaeal ribonuclease VapC1. Budding yeast Nob1 is involved in proteasomal and 40S ribosomal subunit biogenesis. VapC1 is a toxic component and a ribonuclease of a toxin-antitoxin (TA) module. PIN domains are small protein domains identified by the presence of three strictly conserved acidic residues. Apart from these three residues, there is poor sequence conservation. PIN domains are found in eukaryotes, eubacteria and archaea. In eukaryotes they are ribonucleases involved in nonsense mediated mRNA decay and in processing of 18S ribosomal RNA. In prokaryotes, they are the toxic components of toxin-antitoxin (TA) systems, their toxicity arising by virtue of their ribonuclease activity. The PIN domain TA systems are now called VapBC TAs(virulence associated proteins), where VapB is the inhibitor and VapC, the PIN-domain ribonuclease toxin.


Pssm-ID: 465362  Cd Length: 87  Bit Score: 64.73  E-value: 1.51e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726    5 VYDASAFYAGIPF-ASPEIGLTTTVIFEEIKHIKQRHgALDTLLDtdRLRIKDPLKSSIDVVMNAAKKTGDAQKLSKADI 83
Cdd:pfam17146   2 VLDTGAFIKNSTLqALAENIYTTPSVVSEIRDKRTRR-RLETLPY--FLKVREPSPESIKKVTEFAKKTGDYAVLSATDI 78


                  ....*....
gi 785769726   84 SAVALAHEI 92
Cdd:pfam17146  79 EVLALTYEL 87
 
Name Accession Description Interval E-value
Nob1 COG1439
rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis];
1-158 1.53e-68

rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441048 [Multi-domain]  Cd Length: 155  Bit Score: 204.70  E-value: 1.53e-68
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726   1 MASRVYDASAFYAGIPFasPEIGLTTTVIFEEIKHIKQRHgALDtLLDTDRLRIKDPLKSSIDVVMNAAKKTGDAQKLSK 80
Cdd:COG1439    1 MMMYVLDASAFIAGYPL--DGELYTTPSVIEELKDIKSRL-RLE-ALEGGGLRIREPDPESIEKVKKAARKTGDLEELSK 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 785769726  81 ADISAVALAHEIKGNLVTDDFAVSNLAKNLGLQVNPIMTKGIKDVGHWIHYCVGCSKEFS-GLEFCPNCGNKLSRRLLK 158
Cdd:COG1439   77 TDISVLALALELDATLVTDDYALQNVAKHLGIKVEPIATKGIKEVRKWRYRCTGCGREFDePEEECPICGSPLKRKRKK 155
PRK12496 PRK12496
hypothetical protein; Provisional
 4-161 1.59e-40

hypothetical protein; Provisional


Pssm-ID: 237118 [Multi-domain]  Cd Length: 164  Bit Score: 133.98  E-value: 1.59e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726   4 RVYDASAFYAGIPFASPEiGLTTTVIFEEIKHIKQRHgALDTLLDTDRLRIKDPLKSSIDVVMNAAKKTGDAQKLSKADI 83
Cdd:PRK12496   4 KVLDASAFIHGYNPEDGE-HYTTPSVVEEVKDKESRL-ILESAISAGKLKILEPSPESIEKVEEAAIKTGDLMRLSNTDI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726  84 SAVALAHEIKGNLVTDDFAVSNLAKNLGLQVNPIMTKGIKDVGHWIHYCVGCSKEFSGL---EFCPNCGNKLSRRLLKGK 160
Cdd:PRK12496  82 EVLALALELNGTLYTDDYGIQNVAKKLNIKFENIKTKGIKKVIKWRKVCKGCKKKYPEDypdDVCEICGSPVKRKMVKRR 161


                 .
gi 785769726 161 S 161
Cdd:PRK12496 162 L 162
PIN_Nob1-like cd09876
VapC-like PIN domain of eukaryotic ribosome assembly factor Nob1 and archaeal UPF0129 protein ...
 5-117 2.30e-33

VapC-like PIN domain of eukaryotic ribosome assembly factor Nob1 and archaeal UPF0129 protein Ta0041-like homologs; PIN (PilT N terminus) domain of the Saccharomyces cerevisiae ribosome assembly factor, Nob1 (Nin one binding) protein, the Thermoplasma acidophilum DSM 1728, UPF0129 protein Ta0041, and similar eukaryotic and archaeal homologs are included in this family. The Nob1 PIN domain binds the single-stranded cleavage site D at the 3-prime end of 18S rRNA. Recombinant Nob1 binds as a tetramer to pre-18S rRNA fragments containing cleavage site D and believed to cleave at this site. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. 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. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_6.


Pssm-ID: 350224  Cd Length: 112  Bit Score: 113.76  E-value: 2.30e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726   5 VYDASAFYAGIPFASPEIGL-TTTVIFEEIKHIKQRHgALDTLLDtdRLRIKDPLKSSIDVVMNAAKKTGDAQKLSKADI 83
Cdd:cd09876    2 VLDTSAFISGAPLDGLAEKLyTTPEVLEEIRDKKSRL-RLELLPG--KLKVREPSEESIKAVKEFAKKTGDYGSLSATDI 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 785769726  84 SAVALAHEIKGNLVTDDFAVSNLAKNLGLQVNPI 117
Cdd:cd09876   79 KVLALALELEAEIVTDDYAIQNVAKHLGIKFKSI 112
PIN_6 pfam17146
PIN domain of ribonuclease; This is a PIN domain found in eukaryotic ribonuclease Nob1 and ...
 5-92 1.51e-14

PIN domain of ribonuclease; This is a PIN domain found in eukaryotic ribonuclease Nob1 and archaeal ribonuclease VapC1. Budding yeast Nob1 is involved in proteasomal and 40S ribosomal subunit biogenesis. VapC1 is a toxic component and a ribonuclease of a toxin-antitoxin (TA) module. PIN domains are small protein domains identified by the presence of three strictly conserved acidic residues. Apart from these three residues, there is poor sequence conservation. PIN domains are found in eukaryotes, eubacteria and archaea. In eukaryotes they are ribonucleases involved in nonsense mediated mRNA decay and in processing of 18S ribosomal RNA. In prokaryotes, they are the toxic components of toxin-antitoxin (TA) systems, their toxicity arising by virtue of their ribonuclease activity. The PIN domain TA systems are now called VapBC TAs(virulence associated proteins), where VapB is the inhibitor and VapC, the PIN-domain ribonuclease toxin.


Pssm-ID: 465362  Cd Length: 87  Bit Score: 64.73  E-value: 1.51e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726    5 VYDASAFYAGIPF-ASPEIGLTTTVIFEEIKHIKQRHgALDTLLDtdRLRIKDPLKSSIDVVMNAAKKTGDAQKLSKADI 83
Cdd:pfam17146   2 VLDTGAFIKNSTLqALAENIYTTPSVVSEIRDKRTRR-RLETLPY--FLKVREPSPESIKKVTEFAKKTGDYAVLSATDI 78


                  ....*....
gi 785769726   84 SAVALAHEI 92
Cdd:pfam17146  79 EVLALTYEL 87
COG2405 COG2405
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 24-114 2.69e-06

Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only];


Pssm-ID: 441961 [Multi-domain]  Cd Length: 164  Bit Score: 44.86  E-value: 2.69e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 785769726  24 LTTTVIFEEIKHIKQRHGALDTLLDTDRLRIKDPLKSSIDVVMNaakktgdaQKLSKADISAVALAHEIKGN-LVTDDFA 102
Cdd:COG2405   31 IIPEAVYEEIEAGGAPEPGAEELERPGWLEVVEVEDESLVELLR--------KGLDAGEAEAIALALELGADlLLIDDRA 102

                         90
                 ....*....|..
gi 785769726 103 VSNLAKNLGLQV 114
Cdd:COG2405  103 ARKVAKKLGLKV 114
NOB1_Zn_bind pfam08772
Nin one binding (NOB1) Zn-ribbon like; This domain corresponds to a zinc ribbon and is found ...
 122-151 3.14e-03

Nin one binding (NOB1) Zn-ribbon like; This domain corresponds to a zinc ribbon and is found on the RNA binding protein NOB1 (Nin one binding).


Pssm-ID: 462597  Cd Length: 72  Bit Score: 34.80  E-value: 3.14e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 785769726  122 IKDVGHWIHYCVGCSKEFS--GLEFCPNCGNK 151
Cdd:pfam08772   1 IRRVKSWVLRCHACFKVTKdmTKQFCPKCGNA 32
PIN_VapC-like cd18691
uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily; VapC ...
 79-113 4.27e-03

uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily; VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) 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. Some members of the superfamily 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: 350258  Cd Length: 130  Bit Score: 35.58  E-value: 4.27e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 785769726  79 SKADISAVALAHEIKGNLVTDDFAVSNLAKNLGLQ 113
Cdd:cd18691   93 SKEDLDLLLLAKELDAALVSADEGVIKWAEKLGVK 127
 
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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