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Conserved domains on  [gi|624389478|gb|KBT48315|]
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toxin VapC25 [Mycobacterium tuberculosis 2233BH]

Protein Classification

type II toxin-antitoxin system VapC family toxin( domain architecture ID 13036737)

type II toxin-antitoxin (TA) system VapC family toxin functions as a ribonuclease that is neutralized by its cognate antitoxin VapB

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_MtVapC25_VapC33-like cd18678
VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins; This ...
 3-142 6.61e-63

VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC25, VapC29, VapC33, VapC37, and VapC39 toxins. 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: 350245  Cd Length: 140  Bit Score: 188.82  E-value: 6.61e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478   3 LLDANVLLAAHRGDHPNHRTVRPWFDRLLAADDPFTVPNLVWASFLRLTTNRRIFEIPSPRADAFAFVEAVNAQPHHLPT 82
Cdd:cd18678    1 LPDVNVLIYAVRTDHPHHRAAAAWLDAMVSGDDRFGLTPLVLSGFVRIVTNPRVFAAPSPRADAIAQVEAWRAQPNCVLV 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478  83 SPGPRHLVLLRKLCDEADASGDLIPDAVLGAIAVEHHCAVVSLDRDFARFASVRHIRPPI 142
Cdd:cd18678   81 GPGPRHWDILLRLCDEVGAKHRLVTDAYLAALAVEHGCELVTLDRDFARFAGVRWRHPPA 140
 
Name Accession Description Interval E-value
PIN_MtVapC25_VapC33-like cd18678
VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins; This ...
 3-142 6.61e-63

VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC25, VapC29, VapC33, VapC37, and VapC39 toxins. 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: 350245  Cd Length: 140  Bit Score: 188.82  E-value: 6.61e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478   3 LLDANVLLAAHRGDHPNHRTVRPWFDRLLAADDPFTVPNLVWASFLRLTTNRRIFEIPSPRADAFAFVEAVNAQPHHLPT 82
Cdd:cd18678    1 LPDVNVLIYAVRTDHPHHRAAAAWLDAMVSGDDRFGLTPLVLSGFVRIVTNPRVFAAPSPRADAIAQVEAWRAQPNCVLV 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478  83 SPGPRHLVLLRKLCDEADASGDLIPDAVLGAIAVEHHCAVVSLDRDFARFASVRHIRPPI 142
Cdd:cd18678   81 GPGPRHWDILLRLCDEVGAKHRLVTDAYLAALAVEHGCELVTLDRDFARFAGVRWRHPPA 140
Mtu_PIN_fam TIGR00028
toxin-antitoxin system PIN domain toxin; Members of this protein consist almost entirely of a ...
 1-141 1.14e-49

toxin-antitoxin system PIN domain toxin; Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis, but additional members are found now Synechococcus sp. WH8102, etc. Inspection of genomic regions suggests these represent toxin components of toxin-antitoxin regions, potentially important to creating dormant persister cells.


Pssm-ID: 272863  Cd Length: 142  Bit Score: 155.62  E-value: 1.14e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478    1 MFLLDANVLLAAHRGDHPNHRTVRPWFDRLLAADDPFTVPnLVWASFLRLTTNRRIFEIPSPRADAFAFVEAVNAQPHHL 80
Cdd:TIGR00028   1 MLLLDVNVLLAAVNRDHPHHDAARAWLDRFAAGGDWATCP-LTLAGFVRLLTNPRVLPAPLSPAEAIAVVAAFLATPRHR 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 624389478   81 PTSPGPRHLVLLRKLCDEADASGDLIPDAVLGAIAVEHHCAVVSLDRDFARFASVRHIRPP 141
Cdd:TIGR00028  80 LLWPGPRHLAVLRGLADPVIAGGRLVTDAHLAALAREHGAELVTFDRGFARFAGIRWRDPL 140
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 1-140 1.20e-19

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


Pssm-ID: 441453  Cd Length: 134  Bit Score: 78.87  E-value: 1.20e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478   1 MFLLDANVLLAAHRGDHPNHRTVRPWFDRLLAADDPFTVPNLVWASFLRLTTNRRifeiPSPRADAFAFVEAVnaQPHHL 80
Cdd:COG1848    1 MILLDTNVLIYALEGDSPFHERARELLERAEEGEEELYTSPLVLAEVLYVLTRPG----GLSLEEARELLEAL--LSNIE 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 624389478  81 PTSPGPRHLVLLRKLCDEADASgdlIPDAVLGAIAVEHHC-AVVSLDRDFARFASVRHIRP 140
Cdd:COG1848   75 VVPVDEEILEEAAELLAKYGLR---LNDALHLATALEHGAdALVTFDRDFARVPGLEVVDP 132
PIN pfam01850
PIN domain;
3-133 2.90e-10

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 54.34  E-value: 2.90e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478    3 LLDANVLLAAHRgDHPNHRTVRPWfdrlLAADDPFTVPNLVWASFLRLTTNRRifeipsPRADAFAFVEAVNAQPHHLPT 82
Cdd:pfam01850   2 VLDTSVLIALLR-GEPLHEAAREL----LEAAGELVTSAIVLAELLYGLNRRL------GLGKAAELVELLLLLSALEVL 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 624389478   83 SPGPRHLVLLRKLCDEADASGdlIPDAVLGAIAVEHHCAVVSLDRDFARFA 133
Cdd:pfam01850  71 PIDAELAEEAAELRLKYGKLG--PNDALIAATAKEHGAKLITFDEDFARVA 119
 
Name Accession Description Interval E-value
PIN_MtVapC25_VapC33-like cd18678
VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins; This ...
 3-142 6.61e-63

VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins; This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC25, VapC29, VapC33, VapC37, and VapC39 toxins. 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: 350245  Cd Length: 140  Bit Score: 188.82  E-value: 6.61e-63
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478   3 LLDANVLLAAHRGDHPNHRTVRPWFDRLLAADDPFTVPNLVWASFLRLTTNRRIFEIPSPRADAFAFVEAVNAQPHHLPT 82
Cdd:cd18678    1 LPDVNVLIYAVRTDHPHHRAAAAWLDAMVSGDDRFGLTPLVLSGFVRIVTNPRVFAAPSPRADAIAQVEAWRAQPNCVLV 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478  83 SPGPRHLVLLRKLCDEADASGDLIPDAVLGAIAVEHHCAVVSLDRDFARFASVRHIRPPI 142
Cdd:cd18678   81 GPGPRHWDILLRLCDEVGAKHRLVTDAYLAALAVEHGCELVTLDRDFARFAGVRWRHPPA 140
Mtu_PIN_fam TIGR00028
toxin-antitoxin system PIN domain toxin; Members of this protein consist almost entirely of a ...
 1-141 1.14e-49

toxin-antitoxin system PIN domain toxin; Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis, but additional members are found now Synechococcus sp. WH8102, etc. Inspection of genomic regions suggests these represent toxin components of toxin-antitoxin regions, potentially important to creating dormant persister cells.


Pssm-ID: 272863  Cd Length: 142  Bit Score: 155.62  E-value: 1.14e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478    1 MFLLDANVLLAAHRGDHPNHRTVRPWFDRLLAADDPFTVPnLVWASFLRLTTNRRIFEIPSPRADAFAFVEAVNAQPHHL 80
Cdd:TIGR00028   1 MLLLDVNVLLAAVNRDHPHHDAARAWLDRFAAGGDWATCP-LTLAGFVRLLTNPRVLPAPLSPAEAIAVVAAFLATPRHR 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 624389478   81 PTSPGPRHLVLLRKLCDEADASGDLIPDAVLGAIAVEHHCAVVSLDRDFARFASVRHIRPP 141
Cdd:TIGR00028  80 LLWPGPRHLAVLRGLADPVIAGGRLVTDAHLAALAREHGAELVTFDRGFARFAGIRWRDPL 140
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 1-140 1.20e-19

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


Pssm-ID: 441453  Cd Length: 134  Bit Score: 78.87  E-value: 1.20e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478   1 MFLLDANVLLAAHRGDHPNHRTVRPWFDRLLAADDPFTVPNLVWASFLRLTTNRRifeiPSPRADAFAFVEAVnaQPHHL 80
Cdd:COG1848    1 MILLDTNVLIYALEGDSPFHERARELLERAEEGEEELYTSPLVLAEVLYVLTRPG----GLSLEEARELLEAL--LSNIE 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 624389478  81 PTSPGPRHLVLLRKLCDEADASgdlIPDAVLGAIAVEHHC-AVVSLDRDFARFASVRHIRP 140
Cdd:COG1848   75 VVPVDEEILEEAAELLAKYGLR---LNDALHLATALEHGAdALVTFDRDFARVPGLEVVDP 132
PIN pfam01850
PIN domain;
3-133 2.90e-10

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 54.34  E-value: 2.90e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478    3 LLDANVLLAAHRgDHPNHRTVRPWfdrlLAADDPFTVPNLVWASFLRLTTNRRifeipsPRADAFAFVEAVNAQPHHLPT 82
Cdd:pfam01850   2 VLDTSVLIALLR-GEPLHEAAREL----LEAAGELVTSAIVLAELLYGLNRRL------GLGKAAELVELLLLLSALEVL 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 624389478   83 SPGPRHLVLLRKLCDEADASGdlIPDAVLGAIAVEHHCAVVSLDRDFARFA 133
Cdd:pfam01850  71 PIDAELAEEAAELRLKYGKLG--PNDALIAATAKEHGAKLITFDEDFARVA 119
PIN_VapC-like cd09854
VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, ...
 3-134 2.14e-08

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: 49.58  E-value: 2.14e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478   3 LLDANVLLAAHRGDHpnHRTVRPWFDRLLAADDPFTVPNLVWASFLRLTTNRRIfeipsprADAFAFVEAVNAQPHHLPT 82
Cdd:cd09854    1 VLDTNVLIALLSSEP--ESEAAKELLALLLGDSELVIPPLVLAELLRLLARERG-------ARRALEILELLRALEVVEE 71

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 624389478  83 SPGPRHLVLLRklCDEADASGDLIPDAVLGAIAVEH-HCAVVSLDRDFARFAS 134
Cdd:cd09854   72 EPALAEIALEV--LALGLERGLDFGDALILALAKELgGAVLVTNDRDFRRLAK 122
COG5611 COG5611
Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-136 8.66e-06

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


Pssm-ID: 444342  Cd Length: 128  Bit Score: 42.55  E-value: 8.66e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478   1 MFLLDANVLLAAHRGDHPNH-RTVRPWFDRLLAAdDPFTVPNLVWASF---LrlttnRRIFEIPSPR-ADAFAfveavna 75
Cdd:COG5611    1 MIAIDTNVLVRYLTQDDPEQaAKARRLLEQLTGE-EPLFVPLVVLAETvwvL-----RSVYKLPREEiAEALE------- 67

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 624389478  76 qphHLPTSPG---PRHLVLLRKLCDEADASGDLIpDAVLGAIAVEHHC-AVVSLDRDFARFASVR 136
Cdd:COG5611   68 ---ALLGLPNvvvEDREAVEAALALYAEGGADFA-DALIAARARAAGCePVVTFDRKAAKLAGVR 128
COG2402 COG2402
Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]; ...
 1-132 1.07e-05

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


Pssm-ID: 441958  Cd Length: 135  Bit Score: 42.19  E-value: 1.07e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478   1 MFLLDANVLLAAHRGDHPNHRTVRPWFDRLLAADDPFTVPNLVWASFLRLTTNRRIFEIpspradAFAFVEAVNAQPHHL 80
Cdd:COG2402    1 MIFVDTGALIALFNRRDQYHEAAVELLESLLEGELPLVTTDYVLTETLTLLSRRLGREA------AVKFLDRLRESGGLE 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 624389478  81 PTSPGPRHLVLLRKLCDE-ADASGDLIpDAVLGAIAVEH-HCAVVSLDRDFARF 132
Cdd:COG2402   75 IVPLTEEDFERALELFEKyADKPLSLT-DASSVALMERLgIDEILTFDRDFDQY 127
VapC COG1487
Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];
2-136 1.86e-03

Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];


Pssm-ID: 441096  Cd Length: 128  Bit Score: 36.00  E-value: 1.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478   2 FLLDANVLLAAHRGDHPNhrtVRPWFDRLlaADDPFTVPNLVWA----SFLRLTTNRRifeipspRADAFAFVEAVNAQP 77
Cdd:COG1487    1 YLLDTNVLIDLLRGRPPA---VLAWLAEL--EAGELAISAITLAellyGARRSPDAKR-------RAALEAFLEAFPVLP 68

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 624389478  78 hhlPTSPGPRHLVLLRKLCDEADASGDLiPDAVLGAIAVEHHCAVVSLD-RDFARFASVR 136
Cdd:COG1487   69 ---FDAEAARRAGELRAALRRAGRPIGL-ADLLIAATALAHGLTLVTRNtKDFERIPGLK 124
 
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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