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Conserved domains on  [gi|2564994213|ref|WP_306182064|]
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pyocin knob domain-containing S74 family peptidase [Escherichia coli]

Protein Classification

pyocin knob domain-containing S74 family peptidase( domain architecture ID 15331435)

pyocin knob domain-containing S74 family peptidase with an N-terminal domain similar to R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species, and a C-terminal S74 family serine endopeptidase similar to the chaperone domain of Escherichia coli phage K1F endosialidase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Peptidase_S74 pfam13884
Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the ...
 772-821 4.60e-12

Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the bacteriophage protein endosialidase. It releases itself, via the serine-lysine dyad at the N-terminus, from the remainder of the end-tail-spike. Cleavage occurs after the threonine which is the final residue of the End-tail-spike family, pfam12219. The endosialidase protein forms homotrimeric molecules in bacteriophages. The catalytic dyad allows this portion of the molecule to be cleaved from the more N-terminal region such that the latter can fold and bind to polysialic acid in the bacterial outer envelope.


:

Pssm-ID: 404724  Cd Length: 56  Bit Score: 61.49  E-value: 4.60e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2564994213 772 SDRDLKDDIRVIS-DATKAIRKMNGYTYTLK-----ENGLPYAGVIAQEVMEAIPE 821
Cdd:pfam13884   1 SDRRLKTNIKPIDeNALDKIEQLEPVSYDYKdekgeDGARRHIGVIAQEVEEVFPE 56
pyocin_knob cd19958
knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly ...
 497-583 7.01e-07

knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly repeated structural domain in R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu, and they punch a hole in the bacterial envelope to efficiently kill target cells. The second knob domain may contain regions responsible for determining the killing spectrum. Knob-like domains occur in host-recognition and binding proteins of, not only pyocins, but also phages, such as in phage K1F endosialidase (not represented by this model), where it may interact with sialic acid, the cell surface molecule that is recognized during infection.


:

Pssm-ID: 410997 [Multi-domain]  Cd Length: 80  Bit Score: 47.71  E-value: 7.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564994213 497 TVNLNNLTiiksDAGavkYYICPSSAGGANITNKPdgVTGNFLLRVESTrkvrdSDYANMQTLINSDTKRIYVRFVVNGN 576
Cdd:cd19958     7 TTDLNTLT----TPG---FYYQSANANATTALNYP--VAGAGYLEVYRY-----GGGGVTQIYTPYNSGRIYVRTRYNGT 72


                  ....*..
gi 2564994213 577 WTAWSQV 583
Cdd:cd19958    73 WSAWKEI 79
 
Name Accession Description Interval E-value
Peptidase_S74 pfam13884
Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the ...
 772-821 4.60e-12

Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the bacteriophage protein endosialidase. It releases itself, via the serine-lysine dyad at the N-terminus, from the remainder of the end-tail-spike. Cleavage occurs after the threonine which is the final residue of the End-tail-spike family, pfam12219. The endosialidase protein forms homotrimeric molecules in bacteriophages. The catalytic dyad allows this portion of the molecule to be cleaved from the more N-terminal region such that the latter can fold and bind to polysialic acid in the bacterial outer envelope.


Pssm-ID: 404724  Cd Length: 56  Bit Score: 61.49  E-value: 4.60e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2564994213 772 SDRDLKDDIRVIS-DATKAIRKMNGYTYTLK-----ENGLPYAGVIAQEVMEAIPE 821
Cdd:pfam13884   1 SDRRLKTNIKPIDeNALDKIEQLEPVSYDYKdekgeDGARRHIGVIAQEVEEVFPE 56
Peptidase_S74_CIMCD cd10144
Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F ...
 772-830 7.66e-08

Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F endosialidase and related proteins; This peptidase S74 family includes C-terminal intramolecular chaperone domain (CIMCD) of Escherichia coli phage K1F endosialidase, Bacillus phage GA-1 neck appendage protein, and Bacteriophage T5 L-shaped tail fibre. This domain acts as a molecular chaperone; during virus particle assembly, the CIMCD of phage tailspike proteins induces the homo-trimerization of phage tailspike proteins by chaperoning the formation of a triple beta-helix. Homo-trimeric phage tailspike proteins are then auto-cleaved by the CIMCD domain. This family also includes the peptidase S74 Intramolecular Chaperone Auto-processing (ICA) domain of mammalian Myrf. The ICA domain drives the homo-oligomerization of Myrf in the endoplasmic reticulum (ER) membrane. The homo-oligomeric Myrf is proteolyzed by the ICA domain, releasing its N-terminal fragments from the ER membrane.


Pssm-ID: 381748 [Multi-domain]  Cd Length: 113  Bit Score: 51.55  E-value: 7.66e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2564994213 772 SDRDLKDDIRVISDA-TKAIRKMNGYTYTLK----ENGL---PYAGVIAQEVMEAIPEAVGSFTHYG 830
Cdd:cd10144     1 SDARLKTEIREIDDAeLDAWKKVRFVQYKWKeavaEKGDdarLHFGVIAQEVIAAFEDAGLDAGKYG 67
pyocin_knob cd19958
knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly ...
 497-583 7.01e-07

knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly repeated structural domain in R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu, and they punch a hole in the bacterial envelope to efficiently kill target cells. The second knob domain may contain regions responsible for determining the killing spectrum. Knob-like domains occur in host-recognition and binding proteins of, not only pyocins, but also phages, such as in phage K1F endosialidase (not represented by this model), where it may interact with sialic acid, the cell surface molecule that is recognized during infection.


Pssm-ID: 410997 [Multi-domain]  Cd Length: 80  Bit Score: 47.71  E-value: 7.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564994213 497 TVNLNNLTiiksDAGavkYYICPSSAGGANITNKPdgVTGNFLLRVESTrkvrdSDYANMQTLINSDTKRIYVRFVVNGN 576
Cdd:cd19958     7 TTDLNTLT----TPG---FYYQSANANATTALNYP--VAGAGYLEVYRY-----GGGGVTQIYTPYNSGRIYVRTRYNGT 72


                  ....*..
gi 2564994213 577 WTAWSQV 583
Cdd:cd19958    73 WSAWKEI 79
 
Name Accession Description Interval E-value
Peptidase_S74 pfam13884
Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the ...
 772-821 4.60e-12

Chaperone of endosialidase; This is the very C-terminal, chaperone, domain of the bacteriophage protein endosialidase. It releases itself, via the serine-lysine dyad at the N-terminus, from the remainder of the end-tail-spike. Cleavage occurs after the threonine which is the final residue of the End-tail-spike family, pfam12219. The endosialidase protein forms homotrimeric molecules in bacteriophages. The catalytic dyad allows this portion of the molecule to be cleaved from the more N-terminal region such that the latter can fold and bind to polysialic acid in the bacterial outer envelope.


Pssm-ID: 404724  Cd Length: 56  Bit Score: 61.49  E-value: 4.60e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2564994213 772 SDRDLKDDIRVIS-DATKAIRKMNGYTYTLK-----ENGLPYAGVIAQEVMEAIPE 821
Cdd:pfam13884   1 SDRRLKTNIKPIDeNALDKIEQLEPVSYDYKdekgeDGARRHIGVIAQEVEEVFPE 56
Peptidase_S74_CIMCD cd10144
Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F ...
 772-830 7.66e-08

Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F endosialidase and related proteins; This peptidase S74 family includes C-terminal intramolecular chaperone domain (CIMCD) of Escherichia coli phage K1F endosialidase, Bacillus phage GA-1 neck appendage protein, and Bacteriophage T5 L-shaped tail fibre. This domain acts as a molecular chaperone; during virus particle assembly, the CIMCD of phage tailspike proteins induces the homo-trimerization of phage tailspike proteins by chaperoning the formation of a triple beta-helix. Homo-trimeric phage tailspike proteins are then auto-cleaved by the CIMCD domain. This family also includes the peptidase S74 Intramolecular Chaperone Auto-processing (ICA) domain of mammalian Myrf. The ICA domain drives the homo-oligomerization of Myrf in the endoplasmic reticulum (ER) membrane. The homo-oligomeric Myrf is proteolyzed by the ICA domain, releasing its N-terminal fragments from the ER membrane.


Pssm-ID: 381748 [Multi-domain]  Cd Length: 113  Bit Score: 51.55  E-value: 7.66e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2564994213 772 SDRDLKDDIRVISDA-TKAIRKMNGYTYTLK----ENGL---PYAGVIAQEVMEAIPEAVGSFTHYG 830
Cdd:cd10144     1 SDARLKTEIREIDDAeLDAWKKVRFVQYKWKeavaEKGDdarLHFGVIAQEVIAAFEDAGLDAGKYG 67
pyocin_knob cd19958
knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly ...
 497-583 7.01e-07

knob domain of R1 and R2 pyocins and similar domains; The knob domain is present as a tandemly repeated structural domain in R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu, and they punch a hole in the bacterial envelope to efficiently kill target cells. The second knob domain may contain regions responsible for determining the killing spectrum. Knob-like domains occur in host-recognition and binding proteins of, not only pyocins, but also phages, such as in phage K1F endosialidase (not represented by this model), where it may interact with sialic acid, the cell surface molecule that is recognized during infection.


Pssm-ID: 410997 [Multi-domain]  Cd Length: 80  Bit Score: 47.71  E-value: 7.01e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564994213 497 TVNLNNLTiiksDAGavkYYICPSSAGGANITNKPdgVTGNFLLRVESTrkvrdSDYANMQTLINSDTKRIYVRFVVNGN 576
Cdd:cd19958     7 TTDLNTLT----TPG---FYYQSANANATTALNYP--VAGAGYLEVYRY-----GGGGVTQIYTPYNSGRIYVRTRYNGT 72


                  ....*..
gi 2564994213 577 WTAWSQV 583
Cdd:cd19958    73 WSAWKEI 79
 
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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