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Conserved domains on  [gi|17510345|ref|NP_491090|]
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RNA-binding protein NOB1 [Caenorhabditis elegans]

Protein Classification

NOB1 family endonuclease( domain architecture ID 12182052)

uncharacterized NOB1 (nin one binding) family endonuclease similar to Saccharomyces cerevisiae endonuclease NOB1 which is required for cleavage of the 20S pre-RNA at its 3' end (the D-site) to yield the mature 18S RNA; includes a PIN domain

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_6 pfam17146
PIN domain of ribonuclease; This is a PIN domain found in eukaryotic ribonuclease Nob1 and ...
 11-97 7.14e-38

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: 130.99  E-value: 7.14e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345    11 LVIDTCAIIANRNLHALADHYYAPPQILDELRSSAARKLWNTLPFEVTLREPTQTALRAVIDASKTTGDFQSLSMVDIKM 90
Cdd:pfam17146   1 LVLDTGAFIKNSTLQALAENIYTTPSVVSEIRDKRTRRRLETLPYFLKVREPSPESIKKVTEFAKKTGDYAVLSATDIEV 80


                  ....*..
gi 17510345    91 IALTYDL 97
Cdd:pfam17146  81 LALTYEL 87
NOB1_Zn_bind pfam08772
Nin one binding (NOB1) Zn-ribbon like; This domain corresponds to a zinc ribbon and is found ...
 224-295 1.99e-35

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: 123.78  E-value: 1.99e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17510345   224 IRKLKSFVLRCRTCFSTTSVMTKEFCPACGHKTLHKCAVSVDEDGNQQLHINWNRMANRRGLVYTLANPKGG 295
Cdd:pfam08772   1 IRRVKSWVLRCHACFKVTKDMTKQFCPKCGNATLRRVSVSVDEDGTLKLHLKKNFQWNTRGTKYSIPKPKGG 72
 
Name Accession Description Interval E-value
PIN_6 pfam17146
PIN domain of ribonuclease; This is a PIN domain found in eukaryotic ribonuclease Nob1 and ...
 11-97 7.14e-38

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: 130.99  E-value: 7.14e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345    11 LVIDTCAIIANRNLHALADHYYAPPQILDELRSSAARKLWNTLPFEVTLREPTQTALRAVIDASKTTGDFQSLSMVDIKM 90
Cdd:pfam17146   1 LVLDTGAFIKNSTLQALAENIYTTPSVVSEIRDKRTRRRLETLPYFLKVREPSPESIKKVTEFAKKTGDYAVLSATDIEV 80


                  ....*..
gi 17510345    91 IALTYDL 97
Cdd:pfam17146  81 LALTYEL 87
PIN_Nob1-like cd09876
VapC-like PIN domain of eukaryotic ribosome assembly factor Nob1 and archaeal UPF0129 protein ...
 11-102 1.45e-35

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: 125.70  E-value: 1.45e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345  11 LVIDTCAIIANRNLHALADHYYAPPQILDELRSSAARKLWNTLPFEVTLREPTQTALRAVIDASKTTGDFQSLSMVDIKM 90
Cdd:cd09876   1 LVLDTSAFISGAPLDGLAEKLYTTPEVLEEIRDKKSRLRLELLPGKLKVREPSEESIKAVKEFAKKTGDYGSLSATDIKV 80

                        90
                ....*....|..
gi 17510345  91 IALTYDLHRQYV 102
Cdd:cd09876  81 LALALELEAEIV 92
NOB1_Zn_bind pfam08772
Nin one binding (NOB1) Zn-ribbon like; This domain corresponds to a zinc ribbon and is found ...
 224-295 1.99e-35

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: 123.78  E-value: 1.99e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17510345   224 IRKLKSFVLRCRTCFSTTSVMTKEFCPACGHKTLHKCAVSVDEDGNQQLHINWNRMANRRGLVYTLANPKGG 295
Cdd:pfam08772   1 IRRVKSWVLRCHACFKVTKDMTKQFCPKCGNATLRRVSVSVDEDGTLKLHLKKNFQWNTRGTKYSIPKPKGG 72
Nob1 COG1439
rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis];
9-255 9.33e-16

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


Pssm-ID: 441048 [Multi-domain]  Cd Length: 155  Bit Score: 73.74  E-value: 9.33e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345   9 KHLVIDTCAIIANRNLhalADHYYAPPQILDELRSSAARKLWNTLPFE-VTLREPTQTALRAVIDASKTTGDFQSLSMVD 87
Cdd:COG1439   2 MMYVLDASAFIAGYPL---DGELYTTPSVIEELKDIKSRLRLEALEGGgLRIREPDPESIEKVKKAARKTGDLEELSKTD 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345  88 IKMIALTYDLHrqyvaendvaetteddekkniedlsakveqVTVgentedtkeeeieeneesedsavsegsessessesf 167
Cdd:COG1439  79 ISVLALALELD------------------------------ATL------------------------------------ 92

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345 168 dedgwitqdnieetlkklgafeieenmlvgcLTTDFALQNVLLAMNLSLVSLSGYRIRKLKSFVLRCRTCfSTTSVMTKE 247
Cdd:COG1439  93 -------------------------------VTDDYALQNVAKHLGIKVEPIATKGIKEVRKWRYRCTGC-GREFDEPEE 140


                ....*...
gi 17510345 248 FCPACGHK 255
Cdd:COG1439 141 ECPICGSP 148
PRK12496 PRK12496
hypothetical protein; Provisional
 9-98 1.53e-10

hypothetical protein; Provisional


Pssm-ID: 237118 [Multi-domain]  Cd Length: 164  Bit Score: 59.25  E-value: 1.53e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345    9 KHLVIDTCAIIANRNLhaLADHYYAPPQILDELRSSAARKLWNTLPFEVTLR--EPTQTALRAVIDASKTTGDFQSLSMV 86
Cdd:PRK12496   2 MIKVLDASAFIHGYNP--EDGEHYTTPSVVEEVKDKESRLILESAISAGKLKilEPSPESIEKVEEAAIKTGDLMRLSNT 79

                         90
                 ....*....|..
gi 17510345   87 DIKMIALTYDLH 98
Cdd:PRK12496  80 DIEVLALALELN 91
 
Name Accession Description Interval E-value
PIN_6 pfam17146
PIN domain of ribonuclease; This is a PIN domain found in eukaryotic ribonuclease Nob1 and ...
 11-97 7.14e-38

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: 130.99  E-value: 7.14e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345    11 LVIDTCAIIANRNLHALADHYYAPPQILDELRSSAARKLWNTLPFEVTLREPTQTALRAVIDASKTTGDFQSLSMVDIKM 90
Cdd:pfam17146   1 LVLDTGAFIKNSTLQALAENIYTTPSVVSEIRDKRTRRRLETLPYFLKVREPSPESIKKVTEFAKKTGDYAVLSATDIEV 80


                  ....*..
gi 17510345    91 IALTYDL 97
Cdd:pfam17146  81 LALTYEL 87
PIN_Nob1-like cd09876
VapC-like PIN domain of eukaryotic ribosome assembly factor Nob1 and archaeal UPF0129 protein ...
 11-102 1.45e-35

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: 125.70  E-value: 1.45e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345  11 LVIDTCAIIANRNLHALADHYYAPPQILDELRSSAARKLWNTLPFEVTLREPTQTALRAVIDASKTTGDFQSLSMVDIKM 90
Cdd:cd09876   1 LVLDTSAFISGAPLDGLAEKLYTTPEVLEEIRDKKSRLRLELLPGKLKVREPSEESIKAVKEFAKKTGDYGSLSATDIKV 80

                        90
                ....*....|..
gi 17510345  91 IALTYDLHRQYV 102
Cdd:cd09876  81 LALALELEAEIV 92
NOB1_Zn_bind pfam08772
Nin one binding (NOB1) Zn-ribbon like; This domain corresponds to a zinc ribbon and is found ...
 224-295 1.99e-35

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: 123.78  E-value: 1.99e-35
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 17510345   224 IRKLKSFVLRCRTCFSTTSVMTKEFCPACGHKTLHKCAVSVDEDGNQQLHINWNRMANRRGLVYTLANPKGG 295
Cdd:pfam08772   1 IRRVKSWVLRCHACFKVTKDMTKQFCPKCGNATLRRVSVSVDEDGTLKLHLKKNFQWNTRGTKYSIPKPKGG 72
Nob1 COG1439
rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis];
9-255 9.33e-16

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


Pssm-ID: 441048 [Multi-domain]  Cd Length: 155  Bit Score: 73.74  E-value: 9.33e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345   9 KHLVIDTCAIIANRNLhalADHYYAPPQILDELRSSAARKLWNTLPFE-VTLREPTQTALRAVIDASKTTGDFQSLSMVD 87
Cdd:COG1439   2 MMYVLDASAFIAGYPL---DGELYTTPSVIEELKDIKSRLRLEALEGGgLRIREPDPESIEKVKKAARKTGDLEELSKTD 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345  88 IKMIALTYDLHrqyvaendvaetteddekkniedlsakveqVTVgentedtkeeeieeneesedsavsegsessessesf 167
Cdd:COG1439  79 ISVLALALELD------------------------------ATL------------------------------------ 92

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345 168 dedgwitqdnieetlkklgafeieenmlvgcLTTDFALQNVLLAMNLSLVSLSGYRIRKLKSFVLRCRTCfSTTSVMTKE 247
Cdd:COG1439  93 -------------------------------VTDDYALQNVAKHLGIKVEPIATKGIKEVRKWRYRCTGC-GREFDEPEE 140


                ....*...
gi 17510345 248 FCPACGHK 255
Cdd:COG1439 141 ECPICGSP 148
PRK12496 PRK12496
hypothetical protein; Provisional
 9-98 1.53e-10

hypothetical protein; Provisional


Pssm-ID: 237118 [Multi-domain]  Cd Length: 164  Bit Score: 59.25  E-value: 1.53e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17510345    9 KHLVIDTCAIIANRNLhaLADHYYAPPQILDELRSSAARKLWNTLPFEVTLR--EPTQTALRAVIDASKTTGDFQSLSMV 86
Cdd:PRK12496   2 MIKVLDASAFIHGYNP--EDGEHYTTPSVVEEVKDKESRLILESAISAGKLKilEPSPESIEKVEEAAIKTGDLMRLSNT 79

                         90
                 ....*....|..
gi 17510345   87 DIKMIALTYDLH 98
Cdd:PRK12496  80 DIEVLALALELN 91
 
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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