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Conserved domains on  [gi|888573207|emb|CMB00646|]
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Conserved protein of uncharacterised function with PIN domain%2C possible toxin [Mycobacterium tuberculosis]

Protein Classification

type II toxin-antitoxin system VapC family toxin( domain architecture ID 13036763)

type II toxin-antitoxin (TA) system VapC family toxin functions as a ribonuclease that is neutralized by its cognate antitoxin VapB; similar to Mycobacterium tuberculosis ribonuclease VapC26

Gene Ontology:  GO:0004540
PubMed:  28279904|21036780

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_MtVapC26-like cd18696
VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins; Mycobacterium ...
 2-133 1.29e-62

VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins; Mycobacterium tuberculosis VapC26 cleaves 23S rRNA in the Sarcin-Ricin Loop, it is inhibited by the cognate VapB26 antitoxin. This subfamily belongs to the VapC (virulence-associated protein C)-like nuclease family of the PIN domain-like 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: 350263  Cd Length: 132  Bit Score: 187.77  E-value: 1.29e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207   2 IIDTSALLAYFDAAEPDHAAVSECIDSSADALVVSPYVVAELDYLVATRVGVDAELAVLRELAGGAWELANCGAAEIEQA 81
Cdd:cd18696    1 IIDTGALLALFDAADPDHAAVRECIQRSADALVVSPYVVTELDYLLATRVGNDAELAVLQELAGGAFELANCGAAEIEQA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 888573207  82 ARIVTKYQDQRIGIADAANVVLADRYRTRTILTLDRRHFSALRPIGGGRFTV 133
Cdd:cd18696   81 ARIVKKYQDQRIGLADAANVVLADNYGTATILTLDRRHFSALRPIDGSRFTV 132
 
Name Accession Description Interval E-value
PIN_MtVapC26-like cd18696
VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins; Mycobacterium ...
 2-133 1.29e-62

VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins; Mycobacterium tuberculosis VapC26 cleaves 23S rRNA in the Sarcin-Ricin Loop, it is inhibited by the cognate VapB26 antitoxin. This subfamily belongs to the VapC (virulence-associated protein C)-like nuclease family of the PIN domain-like 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: 350263  Cd Length: 132  Bit Score: 187.77  E-value: 1.29e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207   2 IIDTSALLAYFDAAEPDHAAVSECIDSSADALVVSPYVVAELDYLVATRVGVDAELAVLRELAGGAWELANCGAAEIEQA 81
Cdd:cd18696    1 IIDTGALLALFDAADPDHAAVRECIQRSADALVVSPYVVTELDYLLATRVGNDAELAVLQELAGGAFELANCGAAEIEQA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 888573207  82 ARIVTKYQDQRIGIADAANVVLADRYRTRTILTLDRRHFSALRPIGGGRFTV 133
Cdd:cd18696   81 ARIVKKYQDQRIGLADAANVVLADNYGTATILTLDRRHFSALRPIDGSRFTV 132
COG2402 COG2402
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 2-135 1.98e-26

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


Pssm-ID: 441958  Cd Length: 135  Bit Score: 95.73  E-value: 1.98e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207   2 IIDTSALLAYFDAAEPDHAAVSEC---IDSSADALVVSPYVVAELDYLVATRVGVDAELAVLRELAG-GAWELANCGAAE 77
Cdd:COG2402    3 FVDTGALIALFNRRDQYHEAAVELlesLLEGELPLVTTDYVLTETLTLLSRRLGREAAVKFLDRLREsGGLEIVPLTEED 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 888573207  78 IEQAARIVTKYQDQRIGIADAANVVLADRYRTRTILTLDrRHFSALrpigggRFTVIP 135
Cdd:COG2402   83 FERALELFEKYADKPLSLTDASSVALMERLGIDEILTFD-RDFDQY------GFTLLP 133
PIN pfam01850
PIN domain;
1-118 5.12e-03

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 34.69  E-value: 5.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207    1 MIIDTSALLAYFDAaEPDHAAVSECIDSsADALVVSPYVVAELDYLVATRVGVDAELAVLR-ELAGGAWELANCGAAEIE 79
Cdd:pfam01850   1 IVLDTSVLIALLRG-EPLHEAARELLEA-AGELVTSAIVLAELLYGLNRRLGLGKAAELVElLLLLSALEVLPIDAELAE 78

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 888573207   80 QAARIVTKYqdQRIGIADAANVVLADRYRTrTILTLDRR 118
Cdd:pfam01850  79 EAAELRLKY--GKLGPNDALIAATAKEHGA-KLITFDED 114
 
Name Accession Description Interval E-value
PIN_MtVapC26-like cd18696
VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins; Mycobacterium ...
 2-133 1.29e-62

VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins; Mycobacterium tuberculosis VapC26 cleaves 23S rRNA in the Sarcin-Ricin Loop, it is inhibited by the cognate VapB26 antitoxin. This subfamily belongs to the VapC (virulence-associated protein C)-like nuclease family of the PIN domain-like 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: 350263  Cd Length: 132  Bit Score: 187.77  E-value: 1.29e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207   2 IIDTSALLAYFDAAEPDHAAVSECIDSSADALVVSPYVVAELDYLVATRVGVDAELAVLRELAGGAWELANCGAAEIEQA 81
Cdd:cd18696    1 IIDTGALLALFDAADPDHAAVRECIQRSADALVVSPYVVTELDYLLATRVGNDAELAVLQELAGGAFELANCGAAEIEQA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 888573207  82 ARIVTKYQDQRIGIADAANVVLADRYRTRTILTLDRRHFSALRPIGGGRFTV 133
Cdd:cd18696   81 ARIVKKYQDQRIGLADAANVVLADNYGTATILTLDRRHFSALRPIDGSRFTV 132
COG2402 COG2402
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 2-135 1.98e-26

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


Pssm-ID: 441958  Cd Length: 135  Bit Score: 95.73  E-value: 1.98e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207   2 IIDTSALLAYFDAAEPDHAAVSEC---IDSSADALVVSPYVVAELDYLVATRVGVDAELAVLRELAG-GAWELANCGAAE 77
Cdd:COG2402    3 FVDTGALIALFNRRDQYHEAAVELlesLLEGELPLVTTDYVLTETLTLLSRRLGREAAVKFLDRLREsGGLEIVPLTEED 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 888573207  78 IEQAARIVTKYQDQRIGIADAANVVLADRYRTRTILTLDrRHFSALrpigggRFTVIP 135
Cdd:COG2402   83 FERALELFEKYADKPLSLTDASSVALMERLGIDEILTFD-RDFDQY------GFTLLP 133
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 1-118 9.67e-09

VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN domain [Defense mechanisms];


Pssm-ID: 441453  Cd Length: 134  Bit Score: 50.36  E-value: 9.67e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207   1 MIIDTSALLAYFDAAEPDHAAVS---ECIDSSADALVVSPYVVAELDYLVATRVGVDAELA--VLRELAGGaWELANCGA 75
Cdd:COG1848    2 ILLDTNVLIYALEGDSPFHERARellERAEEGEEELYTSPLVLAEVLYVLTRPGGLSLEEAreLLEALLSN-IEVVPVDE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 888573207  76 AEIEQAARIVTKYqdqRIGIADAANVVLADRYRTRTILTLDRR 118
Cdd:COG1848   81 EILEEAAELLAKY---GLRLNDALHLATALEHGADALVTFDRD 120
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 2-131 1.48e-07

VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, rRNA-processing protein Fcf1, Archaeoglobus fulgidus AF0591 protein, and homologs; PIN (PilT N terminus) domains of such ribonucleases as the 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, are included in VapC-like this family. Also included are the PIN domains of the Pyrobaculum aerophilum Pea0151 and Archaeoglobus fulgidus AF0591 proteins and other similar archaeal homologs. The PIN 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: 350205  Cd Length: 129  Bit Score: 46.88  E-value: 1.48e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207   2 IIDTSALLAYFDAAEPDHAAV-SECIDSSADALVVSPYVVAELDYLVATRVGVDAELAVLRELAGGAWELANcgAAEIEQ 80
Cdd:cd09854    1 VLDTNVLIALLSSEPESEAAKeLLALLLGDSELVIPPLVLAELLRLLARERGARRALEILELLRALEVVEEE--PALAEI 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 888573207  81 AARIVTKYQDQRIGIADAANVVLADRYRTRTILTLDrRHFSALRPIGGGRF 131
Cdd:cd09854   79 ALEVLALGLERGLDFGDALILALAKELGGAVLVTND-RDFRRLAKLGLKVI 128
PIN_VapC-like cd18689
uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily; VapC ...
 2-116 3.89e-07

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: 350256  Cd Length: 125  Bit Score: 45.71  E-value: 3.89e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207   2 IIDTSALLAYF-DAAEPDHAAVSECIDSSADALVVSPYVVAELDYLVATRVGVDAELAVLRELAGGAWELANCGAAEIEQ 80
Cdd:cd18689    1 VLDSGALLAYFeGEPHKVAKKLIELIKEGKAELYISAINLGEVYYITARKKGEEKAEEVLSLLLALPIEVVEADEELVEA 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 888573207  81 AARIVTKYqdqRIGIADAANVVLAdRYRTRTILTLD 116
Cdd:cd18689   81 AAKIKAKY---GLSYADCFALATA-KELNAALVTGD 112
PIN_MtVapC20-like cd18680
VapC-like PIN domain of Mycobacterium tuberculosis VapC20 and related proteins; M. ...
 3-116 3.80e-06

VapC-like PIN domain of Mycobacterium tuberculosis VapC20 and related proteins; M. tuberculosis VapC20 inhibits translation by site-specific cleavage of the universally conserved Sarcin-Ricin loop in 23S rRNA. This subfamily belongs to the VapC (virulence-associated protein C)-like nuclease family of the PIN domain-like 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.


Pssm-ID: 350247  Cd Length: 131  Bit Score: 43.22  E-value: 3.80e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207   3 IDTSALLAYFDAAEPDHA-AVS--ECIDSSADALVVSPYVVAELDYLVATRVGVDAELAVLRELAGGAWEL-ANCGAAEI 78
Cdd:cd18680    2 IDTSALIALFNKRDKNHEtAVSyfESAVTGGIRFVVSRPVLMETLNGLSKRYGKRAAVELYDIILSSRFVIiENETEEDW 81

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 888573207  79 EQAARIVTKYQDQR-IGIADAANVVLADRYRTRTILTLD 116
Cdd:cd18680   82 EKAWEIFEKYDDQRgMDFVDALSFAIMERLGIRKAFTFD 120
PIN_MtVapC28-VapC30-like cd09871
VapC-like PIN domain of Mycobacterium tuberculosis VapC28 and 30 and related proteins; This ...
 1-63 3.09e-04

VapC-like PIN domain of Mycobacterium tuberculosis VapC28 and 30 and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC28 and VapC30 toxins. M. tuberculosis VapC28 and VapC30 both cleave tRNA25Ser-TGA and tRNA28Ser-CGA. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a 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.


Pssm-ID: 350219  Cd Length: 128  Bit Score: 37.83  E-value: 3.09e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 888573207   1 MIIDTSALLAYFdAAEPDHAAVSECIDsSADALVVSPYVVAELdYLVATRVGVDAELAVLREL 63
Cdd:cd09871    1 MVVDTSALVAIL-LGEPEAERFLAALA-AAPRRLISAATLVEA-AIVLERRRGPEARSELDEL 60
VapC COG3742
VapC family ribonuclease, contains PIN domain [Defense mechanisms];
1-83 5.17e-04

VapC family ribonuclease, contains PIN domain [Defense mechanisms];


Pssm-ID: 442956  Cd Length: 129  Bit Score: 37.47  E-value: 5.17e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207   1 MIIDTSALLAYFdAAEPDHAAVSECIdSSADALVVSPYVVAELDYLVATRVGVDAELAVLRELAGGAWELANCGAAEIEQ 80
Cdd:COG3742    1 MVVDTSALVAIL-LGEPEAEALAAAL-EAAPPRLISAVTVLEAAIVLARRRGPEARRELDALLAELGIEVVPVDAAQARL 78


                 ...
gi 888573207  81 AAR 83
Cdd:COG3742   79 ARE 81
PIN pfam01850
PIN domain;
1-118 5.12e-03

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 34.69  E-value: 5.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 888573207    1 MIIDTSALLAYFDAaEPDHAAVSECIDSsADALVVSPYVVAELDYLVATRVGVDAELAVLR-ELAGGAWELANCGAAEIE 79
Cdd:pfam01850   1 IVLDTSVLIALLRG-EPLHEAARELLEA-AGELVTSAIVLAELLYGLNRRLGLGKAAELVElLLLLSALEVLPIDAELAE 78

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 888573207   80 QAARIVTKYqdQRIGIADAANVVLADRYRTrTILTLDRR 118
Cdd:pfam01850  79 EAAELRLKY--GKLGPNDALIAATAKEHGA-KLITFDED 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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