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Conserved domains on  [gi|502306617|ref|WP_012758337|]
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type II toxin-antitoxin system VapC family toxin [Rhizobium leguminosarum]

Protein Classification

type II toxin-antitoxin system VapC family toxin( domain architecture ID 10007942)

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 VapC16/VapC22

Gene Ontology:  GO:0004540
PubMed:  28279904|21036780

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG3744 COG3744
PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];
3-128 3.84e-46

PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];


:

Pssm-ID: 442958  Cd Length: 128  Bit Score: 145.74  E-value: 3.84e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617   3 SLLLDTHAWAWSLTGDERLSAKAIALIEKAE-TIFVSPISLFEIGQKVRLGKWPEMEPFIGRLPELLHEQGGIAAALTPE 81
Cdd:COG3744    2 KLLLDTHALLWWLLGDERLSPAARELIEDPAnELYVSAASLWEIAIKVRLGKLDLPEDLDEWLEELLEELGFELLPITPE 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 502306617  82 ICLTAAMMDWTHRDPFDRFLAATAMQNGIPLISADAIFDNLVGNQLW 128
Cdd:COG3744   82 HALAAAQLPLHHRDPFDRLLIAQALVEGLPLVTADRKIAAYGVKTIW 128
 
Name Accession Description Interval E-value
COG3744 COG3744
PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];
3-128 3.84e-46

PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];


Pssm-ID: 442958  Cd Length: 128  Bit Score: 145.74  E-value: 3.84e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617   3 SLLLDTHAWAWSLTGDERLSAKAIALIEKAE-TIFVSPISLFEIGQKVRLGKWPEMEPFIGRLPELLHEQGGIAAALTPE 81
Cdd:COG3744    2 KLLLDTHALLWWLLGDERLSPAARELIEDPAnELYVSAASLWEIAIKVRLGKLDLPEDLDEWLEELLEELGFELLPITPE 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 502306617  82 ICLTAAMMDWTHRDPFDRFLAATAMQNGIPLISADAIFDNLVGNQLW 128
Cdd:COG3744   82 HALAAAQLPLHHRDPFDRLLIAQALVEGLPLVTADRKIAAYGVKTIW 128
PIN_Sll0205-like cd09872
VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC) ...
 5-128 1.63e-45

VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Synechocystis sp. (strain PCC 6803) Sll0205 protein and other uncharacterized homologs are included in this subfamily. They are similar to the PIN domains of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and FitAB, respectively, which are believed to be involved in growth inhibition by regulating translation. These toxins are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the protein complex activates the ribonuclease activity of the toxin by an, as yet undefined mechanism. 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: 350220  Cd Length: 125  Bit Score: 144.15  E-value: 1.63e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617   5 LLDTHAWAWSLTGDERLSAKAIALIE-KAETIFVSPISLFEIGQKVRLGKWPEMEPFIGRLPELLHEQGGIAAALTPEIC 83
Cdd:cd09872    1 LLDTHALLWWLTDPPRLSPKARALIEdPANEVFVSAASLWEIAIKVSLGKLDLPGPLEEWLEELLAANGFEILPITPEHA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 502306617  84 LTAAMMDWTHRDPFDRFLAATAMQNGIPLISADAIFDNLVGNQLW 128
Cdd:cd09872   81 LAAASLPLHHRDPFDRLLIAQAIVEGLTLVTADRKILAYGVKTIW 125
PIN pfam01850
PIN domain;
4-122 6.63e-11

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 55.49  E-value: 6.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617    4 LLLDTHAWAWsLTGDERLSAKAIALIEKAETIFVSPISLFEIGQKVRLGKWPEMEPFIGRLPELLheQGGIAAALTPEIC 83
Cdd:pfam01850   1 IVLDTSVLIA-LLRGEPLHEAARELLEAAGELVTSAIVLAELLYGLNRRLGLGKAAELVELLLLL--SALEVLPIDAELA 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 502306617   84 LTAAMMDWTHR--DPFDRFLAATAMQNGIPLISADAIFDNL 122
Cdd:pfam01850  78 EEAAELRLKYGklGPNDALIAATAKEHGAKLITFDEDFARV 118
 
Name Accession Description Interval E-value
COG3744 COG3744
PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];
3-128 3.84e-46

PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];


Pssm-ID: 442958  Cd Length: 128  Bit Score: 145.74  E-value: 3.84e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617   3 SLLLDTHAWAWSLTGDERLSAKAIALIEKAE-TIFVSPISLFEIGQKVRLGKWPEMEPFIGRLPELLHEQGGIAAALTPE 81
Cdd:COG3744    2 KLLLDTHALLWWLLGDERLSPAARELIEDPAnELYVSAASLWEIAIKVRLGKLDLPEDLDEWLEELLEELGFELLPITPE 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 502306617  82 ICLTAAMMDWTHRDPFDRFLAATAMQNGIPLISADAIFDNLVGNQLW 128
Cdd:COG3744   82 HALAAAQLPLHHRDPFDRLLIAQALVEGLPLVTADRKIAAYGVKTIW 128
PIN_Sll0205-like cd09872
VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC) ...
 5-128 1.63e-45

VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Synechocystis sp. (strain PCC 6803) Sll0205 protein and other uncharacterized homologs are included in this subfamily. They are similar to the PIN domains of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and FitAB, respectively, which are believed to be involved in growth inhibition by regulating translation. These toxins are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the protein complex activates the ribonuclease activity of the toxin by an, as yet undefined mechanism. 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: 350220  Cd Length: 125  Bit Score: 144.15  E-value: 1.63e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617   5 LLDTHAWAWSLTGDERLSAKAIALIE-KAETIFVSPISLFEIGQKVRLGKWPEMEPFIGRLPELLHEQGGIAAALTPEIC 83
Cdd:cd09872    1 LLDTHALLWWLTDPPRLSPKARALIEdPANEVFVSAASLWEIAIKVSLGKLDLPGPLEEWLEELLAANGFEILPITPEHA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 502306617  84 LTAAMMDWTHRDPFDRFLAATAMQNGIPLISADAIFDNLVGNQLW 128
Cdd:cd09872   81 LAAASLPLHHRDPFDRLLIAQAIVEGLTLVTADRKILAYGVKTIW 125
PIN_VapC-FitB-like cd09875
VapC-like PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin ...
 5-120 5.07e-12

VapC-like PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs; PIN (PilT N terminus) domain-containing proteins of prokaryotic toxin/antitoxin (TA) operons, such as, Mycobacterium tuberculosis VapC of the VapBC (virulence associated proteins) TA operon, and Neisseria gonorrhoeae FitB of the FitAB (fast intracellular trafficking) TA operon, as well as, the archaeal Pyrococcus horikoshii protein PH0500 are included in this family. Toxins of TA operons are believed to be involved in growth inhibition by regulating translation and are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the complex activates the ribonuclease activity of the toxin. In N. gonorrhoeae, FitA and FitB form a heterodimer: FitA is the DNA binding subunit and FitB contains a ribonuclease activity that is blocked by the presence of FitA. A tetramer of FitAB heterodimers binds DNA from the fitAB upstream promoter region with high affinity. This results in both sequestration of FitAB and repression of fitAB transcription. It is thought that FitAB release from the DNA and subsequent dissociation both slows N. gonorrhoeae replication and transcytosis by an as yet undefined mechanism. The toxin M. tuberculosis VapC is a structural homolog of N. gonorrhoeae FitB, but their antitoxin partners, VapB and FitA, respectively, differ structurally. The M. tuberculosis VapC-5 is proposed to be both an endoribonuclease and an exoribonuclease that can act on free RNA in a similar manner to the endo and exonuclease Flap endonuclease-1 (FEN1). VapC-like toxins are structural homologs of FEN1-like PIN domains, but lack the extensive arch/clamp region and the H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region, seen in FEN1-like PIN domains. PIN domains within this group typically contain three or four conserved acidic residues that cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. These putative active site residues are thought to bind Mg2+ and/or Mn2+ ions and be essential for single-stranded ribonuclease activity. VapC-like PIN domains are single domain proteins that form dimers and dimerization configures the active sites in a groove along the long-axis of the structure.


Pssm-ID: 350223  Cd Length: 130  Bit Score: 58.73  E-value: 5.07e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617   5 LLDTHAWAWSLTGDERLSAKAIALIEKAETIFVSPISLFEIGQKVRLGKWPEMEPFIGRLPELLHEQGGI------AAAL 78
Cdd:cd09875    1 LLDTSVLIWLLDNDPKSHLRSLADRIERGKVYVSIVSRWELAIGVNINKLRLNYAFADLENLLADLAIPVlpltprIADE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 502306617  79 TPEIClTAAMMDWTHRDPFDRFLAATAMQNGIPLISADAIFD 120
Cdd:cd09875   81 YLEAC-RNLPLRGRHRSPFDRMIAAQALQHGFTVAHRDEDFK 121
PIN pfam01850
PIN domain;
4-122 6.63e-11

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 55.49  E-value: 6.63e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617    4 LLLDTHAWAWsLTGDERLSAKAIALIEKAETIFVSPISLFEIGQKVRLGKWPEMEPFIGRLPELLheQGGIAAALTPEIC 83
Cdd:pfam01850   1 IVLDTSVLIA-LLRGEPLHEAARELLEAAGELVTSAIVLAELLYGLNRRLGLGKAAELVELLLLL--SALEVLPIDAELA 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 502306617   84 LTAAMMDWTHR--DPFDRFLAATAMQNGIPLISADAIFDNL 122
Cdd:pfam01850  78 EEAAELRLKYGklGPNDALIAATAKEHGAKLITFDEDFARV 118
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 4-124 1.44e-05

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


Pssm-ID: 441453  Cd Length: 134  Bit Score: 41.51  E-value: 1.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617   4 LLLDTHAWAWSLTGDERLSAKAIALIEKAE----TIFVSPISLFEIGQKV-RLGKWP--EMEPFIGRLPELLHEqggiaA 76
Cdd:COG1848    2 ILLDTNVLIYALEGDSPFHERARELLERAEegeeELYTSPLVLAEVLYVLtRPGGLSleEARELLEALLSNIEV-----V 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 502306617  77 ALTPEICLTAAMMDWTHR-DPFDRFLAATAMQNGIP-LISADAIFDNLVG 124
Cdd:COG1848   77 PVDEEILEEAAELLAKYGlRLNDALHLATALEHGADaLVTFDRDFARVPG 126
VapC COG1487
Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms];
5-117 1.51e-05

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


Pssm-ID: 441096  Cd Length: 128  Bit Score: 41.39  E-value: 1.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617   5 LLDTHAWAWSLTGDERLSAKAIALIEkAETIFVSPISLFEIGQKVRLGKWPEMEP----FIGRLPELlheqggiaaALTP 80
Cdd:COG1487    2 LLDTNVLIDLLRGRPPAVLAWLAELE-AGELAISAITLAELLYGARRSPDAKRRAaleaFLEAFPVL---------PFDA 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 502306617  81 EICLTAAMMDWTHR------DPFDRFLAATAMQNGIPLISADA 117
Cdd:COG1487   72 EAARRAGELRAALRragrpiGLADLLIAATALAHGLTLVTRNT 114
PIN_MtVapC3-like_start cd09882
VapC-like PIN domain of Mycobacterium tuberculosis VapC3 toxin and related proteins; The ...
 5-122 2.29e-05

VapC-like PIN domain of Mycobacterium tuberculosis VapC3 toxin and related proteins; The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, and VapC21. 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 (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: 350230  Cd Length: 128  Bit Score: 41.04  E-value: 2.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617   5 LLDTHAWAWSLTG-DERLSAKAIALIEKAETIFVSPISLFEIGQKVRLGK-WPEMEPFIGRLPELlheqggiaaALTPEI 82
Cdd:cd09882    1 LVDTSVWIDFFRGrDTPQVERLKELIEEGEDVALTGIILTEVLQGIRDEKeFQRVKEYLLALPIL---------PLTGET 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 502306617  83 CLTAA----MMDW---THRDPFDRFLAATAMQNGIPLISADAIFDNL 122
Cdd:cd09882   72 YIAAArlyrRLRRkgvTVRSTIDCLIAATAIENGLTLLHNDRDFEAI 118
PIN_MtVapC3-like cd18765
uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily; ...
 5-122 2.05e-03

uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily; The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. 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: 350332  Cd Length: 131  Bit Score: 35.83  E-value: 2.05e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502306617   5 LLDTHAWAWSLTGDERLSAKAIA-LIEKAETIFVSPISLFEIGQKVR----LGKWPEMEPFIGRLPELLHEQGGIAAALT 79
Cdd:cd18765    1 LVDTSVWIDLLRGTGTPAVRRLRrLLQSEEPVALAPVILQELLQGARspehFVRLQAHFDALPMLKPKDARATHRAAAAL 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 502306617  80 PEICLTAAMmdwTHRDPFDRFLAATAMQNGIPLISADAIFDNL 122
Cdd:cd18765   81 YARCRWAGI---TPRSPNDCLIAQCAIEHGVPLLHDDRDFETI 120
 
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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