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Conserved domains on  [gi|1085407508|gb|OGV76469|]
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MAG: hypothetical protein A3K18_12715 [Lentisphaerae bacterium RIFOXYA12_64_32]

Protein Classification

type II toxin-antitoxin system VapC family toxin( domain architecture ID 10177353)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PIN_Sll0205-like cd09872
VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC) ...
 6-128 7.53e-49

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: 152.24  E-value: 7.53e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085407508   6 LDTCALIWLVNGGDKLSAGTQKTIRD-ASIVFVSAASAIEIGCKAALGRLTLPMAPEEWYRRALEHHGIVELPIDGNTGF 84
Cdd:cd09872     2 LDTHALLWWLTDPPRLSPKARALIEDpANEVFVSAASLWEIAIKVSLGKLDLPGPLEEWLEELLAANGFEILPITPEHAL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1085407508  85 GAARLPMLHRDPADRLIIAAARARGIPVATHDSRFESYGVTVLR 128
Cdd:cd09872    82 AAASLPLHHRDPFDRLLIAQAIVEGLTLVTADRKILAYGVKTIW 125
 
Name Accession Description Interval E-value
PIN_Sll0205-like cd09872
VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC) ...
 6-128 7.53e-49

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: 152.24  E-value: 7.53e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085407508   6 LDTCALIWLVNGGDKLSAGTQKTIRD-ASIVFVSAASAIEIGCKAALGRLTLPMAPEEWYRRALEHHGIVELPIDGNTGF 84
Cdd:cd09872     2 LDTHALLWWLTDPPRLSPKARALIEDpANEVFVSAASLWEIAIKVSLGKLDLPGPLEEWLEELLAANGFEILPITPEHAL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1085407508  85 GAARLPMLHRDPADRLIIAAARARGIPVATHDSRFESYGVTVLR 128
Cdd:cd09872    82 AAASLPLHHRDPFDRLLIAQAIVEGLTLVTADRKILAYGVKTIW 125
COG3744 COG3744
PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];
4-128 9.23e-48

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


Pssm-ID: 442958  Cd Length: 128  Bit Score: 149.60  E-value: 9.23e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085407508   4 LMLDTCALIWLVNGGDKLSAGTQKTIRDAS-IVFVSAASAIEIGCKAALGRLTLPMAPEEWYRRALEHHGIVELPIDGNT 82
Cdd:COG3744     3 LLLDTHALLWWLLGDERLSPAARELIEDPAnELYVSAASLWEIAIKVRLGKLDLPEDLDEWLEELLEELGFELLPITPEH 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1085407508  83 GFGAARLPMLHRDPADRLIIAAARARGIPVATHDSRFESYGVTVLR 128
Cdd:COG3744    83 ALAAAQLPLHHRDPFDRLLIAQALVEGLPLVTADRKIAAYGVKTIW 128
PIN pfam01850
PIN domain;
4-123 6.65e-10

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 52.80  E-value: 6.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085407508   4 LMLDTCALIWLVNGgDKLSAGTQKTIRDASIVFVSAASAIEIGCKAAlgRLTLPMAPEEWYRRALEHHGIVELPIDGNTG 83
Cdd:pfam01850   1 IVLDTSVLIALLRG-EPLHEAARELLEAAGELVTSAIVLAELLYGLN--RRLGLGKAAELVELLLLLSALEVLPIDAELA 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1085407508  84 FGAARLP--MLHRDPADRLIIAAARARGIPVATHDSRFESYG 123
Cdd:pfam01850  78 EEAAELRlkYGKLGPNDALIAATAKEHGAKLITFDEDFARVA 119
 
Name Accession Description Interval E-value
PIN_Sll0205-like cd09872
VapC-like PIN domain of Sll0205 protein and homologs; Virulence associated protein C (VapC) ...
 6-128 7.53e-49

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: 152.24  E-value: 7.53e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085407508   6 LDTCALIWLVNGGDKLSAGTQKTIRD-ASIVFVSAASAIEIGCKAALGRLTLPMAPEEWYRRALEHHGIVELPIDGNTGF 84
Cdd:cd09872     2 LDTHALLWWLTDPPRLSPKARALIEDpANEVFVSAASLWEIAIKVSLGKLDLPGPLEEWLEELLAANGFEILPITPEHAL 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1085407508  85 GAARLPMLHRDPADRLIIAAARARGIPVATHDSRFESYGVTVLR 128
Cdd:cd09872    82 AAASLPLHHRDPFDRLLIAQAIVEGLTLVTADRKILAYGVKTIW 125
COG3744 COG3744
PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms];
4-128 9.23e-48

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


Pssm-ID: 442958  Cd Length: 128  Bit Score: 149.60  E-value: 9.23e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085407508   4 LMLDTCALIWLVNGGDKLSAGTQKTIRDAS-IVFVSAASAIEIGCKAALGRLTLPMAPEEWYRRALEHHGIVELPIDGNT 82
Cdd:COG3744     3 LLLDTHALLWWLLGDERLSPAARELIEDPAnELYVSAASLWEIAIKVRLGKLDLPEDLDEWLEELLEELGFELLPITPEH 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1085407508  83 GFGAARLPMLHRDPADRLIIAAARARGIPVATHDSRFESYGVTVLR 128
Cdd:COG3744    83 ALAAAQLPLHHRDPFDRLLIAQALVEGLPLVTADRKIAAYGVKTIW 128
PIN pfam01850
PIN domain;
4-123 6.65e-10

PIN domain;


Pssm-ID: 426475  Cd Length: 121  Bit Score: 52.80  E-value: 6.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085407508   4 LMLDTCALIWLVNGgDKLSAGTQKTIRDASIVFVSAASAIEIGCKAAlgRLTLPMAPEEWYRRALEHHGIVELPIDGNTG 83
Cdd:pfam01850   1 IVLDTSVLIALLRG-EPLHEAARELLEAAGELVTSAIVLAELLYGLN--RRLGLGKAAELVELLLLLSALEVLPIDAELA 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1085407508  84 FGAARLP--MLHRDPADRLIIAAARARGIPVATHDSRFESYG 123
Cdd:pfam01850  78 EEAAELRlkYGKLGPNDALIAATAKEHGAKLITFDEDFARVA 119
PIN_VapC-FitB-like cd09875
VapC-like PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin ...
 5-122 8.75e-06

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: 42.17  E-value: 8.75e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085407508   5 MLDTCALIWLVNGGDKLSAGTQKTIRDASIVFVSAASAIEIGCKAALGRLTLPMAPEEWYRRALEHHGIVeLPIDGNTGF 84
Cdd:cd09875     1 LLDTSVLIWLLDNDPKSHLRSLADRIERGKVYVSIVSRWELAIGVNINKLRLNYAFADLENLLADLAIPV-LPLTPRIAD 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1085407508  85 GAAR------LPMLHRDPADRLIIAAARARGIPVATHDSRFESY 122
Cdd:cd09875    80 EYLEacrnlpLRGRHRSPFDRMIAAQALQHGFTVAHRDEDFKAI 123
VapC COG1848
VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN ...
 4-128 1.03e-03

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


Pssm-ID: 441453  Cd Length: 134  Bit Score: 36.50  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1085407508   4 LMLDTCALIWLVNGGDKLSAGTQKTIRDAS----IVFVSAASAIEIGCKAA-LGRLTLPMApEEWYRRALEHHGIVelPI 78
Cdd:COG1848     2 ILLDTNVLIYALEGDSPFHERARELLERAEegeeELYTSPLVLAEVLYVLTrPGGLSLEEA-RELLEALLSNIEVV--PV 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1085407508  79 DGNTGFGAARLPMLHR-DPADRLIIAAARARGIP-VATHDSRF-ESYGVTVLR 128
Cdd:COG1848    79 DEEILEEAAELLAKYGlRLNDALHLATALEHGADaLVTFDRDFaRVPGLEVVD 131
 
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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