Protein Family Models

Domain found in multiple copies in kinetoplastid-specific minicircle binding proteins that evolved from a prokaryotic ArdCN domain [1]. 30396152. Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic. NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile. Elements.. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. iScience. 2018;9:192-208. (from Pfam)

Date:

2024-08-14

Phage_holin_2_3 is a family of small hydrophobic phage proteins called holins with one transmembrane domain. Holins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion 1,2]. [1]. 8710508. The complete nucleotide sequence of bacteriophage HP1 DNA.. Esposito D, Fitzmaurice WP, Benjamin RC, Goodman SD, Waldman AS,. Scocca JJ;. Nucleic Acids Res. 1996;24:2360-2368.. [2]. 9068631. Cloning and characterization of bacteriophage-like DNA from. Haemophilus somnus homologous to phages P2 and HP1.. Pontarollo RA, Rioux CR, Potter AA;. J Bacteriol. 1997;179:1872-1879. (from Pfam)

Date:

2024-08-14

This is a SH3-like domain associated with the MutS-like ABC ATPase and Smr domains. It has been predicted to play a role in lesion recognition or alternatively in mediating contacts with RNA primers or misincorporated ribonucleotides during DNA repair or interacting with the ribosome at the intersection between DNA repair and ribosome rescue [1]. [1]. 32894288. Comprehensive classification of ABC ATPases and their functional. radiation in nucleoprotein dynamics and biological conflict. systems.. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. Nucleic Acids Res. 2020;48:10045-10075. (from Pfam)

Date:

2024-08-14

Phage_holin_2_4 is a family of small hydrophobic phage proteins called holins with one transmembrane domain. Holins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion. (from Pfam)

Date:

2024-08-14

Phage_holin_V_2 is a family of small hydrophobic proteins with three transmembrane domains of the Hol44 family. These proteins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion. Full activity of the endolysin Lys44 from oenophage fOg44 requires sudden ion-nonspecific dissipation of the proton motive force, undertaken by the fOg44 holin during phage-infection [1,2,3]. [1]. 9332359. Functional and structural features of the holin HOL protein of. the Lactobacillus plantarum phage phi gle: analysis in. Escherichia coli system.. Oki M, Kakikawa M, Nakamura S, Yamamura ET, Watanabe K, Sasamoto. M, Taketo A, Kodaira K;. Gene. 1997;197:137-145.. [2]. 17322187. The complete genome sequence of Clostridium difficile phage. phiC2 and comparisons to phiCD119 and inducible prophages of. CD630.. Goh S, Ong PF, Song KP, Riley TV, Chang BJ;. Microbiology. 2007;153:676-685.. [3]. 17981964. Nisin-triggered activity of Lys44, the secreted endolysin from. Oenococcus oeni phage fOg44.. Nascimento JG, Guerreiro-Pereira MC, Costa SF, Sao-Jose C,. Santos MA;. J Bacteriol. 2008;190:457-461. (from Pfam)

Date:

2024-08-14

This short domain is found in the Rad4 protein. This domain binds to DNA [1]. [1]. 17882165. Recognition of DNA damage by the Rad4 nucleotide excision repair. protein.. Min JH, Pavletich NP;. Nature. 2007;449:570-575.. [2]. 30396152. Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic. NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile. Elements.. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. iScience. 2018;9:192-208. (from Pfam)

Date:

2024-08-14

This short domain is found in the Rad4 protein. This domain binds to DNA [1]. [1]. 17882165. Recognition of DNA damage by the Rad4 nucleotide excision repair. protein.. Min JH, Pavletich NP;. Nature. 2007;449:570-575.. [2]. 30396152. Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic. NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile. Elements.. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. iScience. 2018;9:192-208. (from Pfam)

Date:

2024-08-14

This short domain is found in the Rad4 protein. This domain binds to DNA [1]. [1]. 17882165. Recognition of DNA damage by the Rad4 nucleotide excision repair. protein.. Min JH, Pavletich NP;. Nature. 2007;449:570-575.. [2]. 30396152. Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic. NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile. Elements.. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. iScience. 2018;9:192-208. (from Pfam)

Date:

2024-08-14

This is the ssDNA binding domain of anti-restriction factor ArdC deployed by plasmids and phages in polyvalent proteins related to the BHD domains of XPC/Rad4 and the Tc-38 domain found in kinetoplastid minicircle binding proteins [1,2,3]. The structure of this domain is composed of three alpha-helices and a three-stranded beta-sheet that supports a long and protuberant beta-hairpin [3]. This domain is also found in the N-terminal region of the RP4 TraC1 primase [4], together with the Toprim domain (pfam:PF01751, pfam:PF13362 and pfam:PF13662). [1]. 30396152. Unexpected Evolution of Lesion-Recognition Modules in Eukaryotic. NER and Kinetoplast DNA Dynamics Proteins from Bacterial Mobile. Elements.. Krishnan A, Burroughs AM, Iyer LM, Aravind L;. iScience. 2018;9:192-208.. [2]. 28559295. Polyvalent Proteins, a Pervasive Theme in the Intergenomic. Biological Conflicts of Bacteriophages and Conjugative Elements.. Iyer LM, Burroughs AM, Anand S, de Souza RF, Aravind L;. J Bacteriol. 2017; [Epub ahead of print]. [3]. 32348296. ArdC, a ssDNA-binding protein with a metalloprotease domain,. overpasses the recipient hsdRMS restriction system broadening. conjugation host range.. Gonzalez-Montes L, Del Campo I, Garcillan-Barcia MP, de la Cruz. F, Moncalian G;. PLoS Genet. 2020;16:e1008750.. [4]. 10686096. Antirestriction protein Ard (Type C) encoded by IncW plasmid pSa. has a high similarity to the "protein transport" domain of TraC1. primase of promiscuous plasmid RP4.. Belogurov AA, Delver EP, Agafonova OV, Belogurova NG, Lee LY,. Kado CI;. J Mol Biol. 2000;296:969-977. (from Pfam)

Date:

2024-08-14

Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localised destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation [1]. This family represents the Tir C-terminal domain which has been reported to bind uninfected host cells and beta-1 integrins although the role of intimin binding to integrins is unclear. This intimin C-terminal domain has also been shown to be sufficient for Tir recognition [2]. [1]. 10890451. Crystal structure of enteropathogenic Escherichia coli. intimin-receptor complex.. Luo Y, Frey EA, Pfuetzner RA, Creagh AL, Knoechel DG, Haynes CA,. Finlay BB, Strynadka NC;. Nature 2000;405:1073-1077.. [2]. 11207537. Identification of the intimin-binding domain of Tir of. enteropathogenic Escherichia coli.. de Grado M, Abe A, Gauthier A, Steele-Mortimer O, DeVinney R,. Finlay BB;. Cell Microbiol 1999;1:7-17. (from Pfam)

Date:

2024-08-14

This family consists of the major transforming proteins (E5) of the bovine papilloma virus (BPV). The equine sarcoid is one of the most common dermatological lesion in equids. It is a benign, locally invasive dermal fibroblastic lesion and studies have shown an association of the lesions with BPV. E5 is a short hydrophobic membrane protein localising to the Golgi apparatus and other intracellular membranes. It binds to and constitutively activates the platelet-derived growth factor-beta in transformed cells. This stimulation activates a receptor signaling cascade which results in an intracellular growth stimulatory signal [1]. [1]. 12951274. Sequence variants of bovine papillomavirus E5 detected in equine. sarcoids.. Chambers G, Ellsmore VA, O'Brien PM, Reid SW, Love S, Campo MS,. Nasir L;. Virus Res 2003;96:141-145. (from Pfam)

Date:

2024-08-14

Phage_holin_3_6 is a family of small hydrophobic proteins with two or three transmembrane domains of the Hol-X family. Holin proteins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion. (from Pfam)

Date:

2024-08-14

Members of this family are DNA glycosylases performing base excision for DNA repair. Substrates include 8-oxoguanine and 3-methyladenine.

Date:

2024-08-14

Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localised destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation [1]. This family represents the Tir N-terminal domain which is involved in Tir stability and Tir secretion [2]. [1]. 10890451. Crystal structure of enteropathogenic Escherichia coli. intimin-receptor complex.. Luo Y, Frey EA, Pfuetzner RA, Creagh AL, Knoechel DG, Haynes CA,. Finlay BB, Strynadka NC;. Nature 2000;405:1073-1077.. [2]. 11207537. Identification of the intimin-binding domain of Tir of. enteropathogenic Escherichia coli.. de Grado M, Abe A, Gauthier A, Steele-Mortimer O, DeVinney R,. Finlay BB;. Cell Microbiol 1999;1:7-17. (from Pfam)

Date:

2024-08-14

HrpZ from the plant pathogen Pseudomonas syringae binds to lipid bilayers and forms a cation-conducting pore in vivo. This pore-forming activity may allow nutrient release or delivery of virulence factors during bacterial colonisation of host plants [1]. The family of hairpinN proteins, Harpin, has been merged into this family. HrpN is a virulence determinant which elicits lesion formation in Arabidopsis and tobacco and triggers systemic resistance in Arabidopsis [2]. [1]. 11134504. HrpZ(Psph) from the plant pathogen Pseudomonas syringae pv.. phaseolicola binds to lipid bilayers and forms an ion-conducting. pore in vitro.. Lee J, Klusener B, Tsiamis G, Stevens C, Neyt C, Tampakaki AP,. Panopoulos NJ, Noller J, Weiler EW, Cornelis GR, Mansfield JW,. Nurnberger T;. Proc Natl Acad Sci U S A 2001;98:289-294.. [2]. 12650449. Erwinia carotovora subsp. carotovora and Erwinia-derived. elicitors HrpN and PehA trigger distinct but interacting defense. responses and cell death in Arabidopsis.. Kariola T, Palomaki TA, Brader G, Palva ET;. Mol Plant Microbe Interact 2003;16:179-187. (from Pfam)

Date:

2024-08-14

Family of plant proteins that are associated with the hypersensitive response (HR) pathway of defence against plant pathogens. (from Pfam)

Date:

2024-08-14

EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system. These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell [1,2]. [1]. 9545230. A novel EspA-associated surface organelle of enteropathogenic. Escherichia coli involved in protein translocation into. epithelial cells.. Knutton S, Rosenshine I, Pallen MJ, Nisan I, Neves BC, Bain C,. Wolff C, Dougan G, Frankel G;. EMBO J 1998;17:2166-2176.. [2]. 10760148. The type III protein translocation system of enteropathogenic. Escherichia coli involves EspA-EspB protein interactions.. Hartland EL, Daniell SJ, Delahay RM, Neves BC, Wallis T, Shaw. RK, Hale C, Knutton S, Frankel G;. Mol Microbiol 2000;35:1483-1492.. [3]. 10047555. Enteropathogenic Escherichia coli: cellular harassment.. DeVinney R, Knoechel DG, Finlay BB;. Curr Opin Microbiol 1999;2:83-88. (from Pfam)

Date:

2024-08-14

Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localised destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation [1]. This family represents the Tir intimin-binding domain (Tir IBD) which is needed to bind intimin and support the predicted topology for Tir, with both N- and C-terminal regions in the mammalian cell cytosol [2]. [1]. 10890451. Crystal structure of enteropathogenic Escherichia coli. intimin-receptor complex.. Luo Y, Frey EA, Pfuetzner RA, Creagh AL, Knoechel DG, Haynes CA,. Finlay BB, Strynadka NC;. Nature 2000;405:1073-1077.. [2]. 11207537. Identification of the intimin-binding domain of Tir of. enteropathogenic Escherichia coli.. de Grado M, Abe A, Gauthier A, Steele-Mortimer O, DeVinney R,. Finlay BB;. Cell Microbiol 1999;1:7-17. (from Pfam)

Date:

2024-08-14

This is the RNA polymerase interacting domain (RID) of transcription-repair-coupling factor (TRCF), CarD and CarD homologue in Myxococcus xanthus, called CdnL. In Myxococcus xanthus, CdnL is a protein required for the activation of light- and starvation-inducible genes [1]. It interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus [4]. CarD is widely distributed among bacteria and represents a distinct class of RNAP binding proteins that regulate transcription and essential processes [4-8]. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription [3]. [1]. 8692912. High mobility group I(Y)-like DNA-binding domains on a bacterial. transcription factor.. Nicolas FJ, Cayuela ML, Martinez-Argudo IM, Ruiz-Vazquez RM,. Murillo FJ;. Proc Natl Acad Sci U S A 1996;93:6881-6885.. [2]. 11533063. Domain architecture of a high mobility group A-type bacterial. transcriptional factor.. Padmanabhan S, Elias-Arnanz M, Carpio E, Aparicio P, Murillo FJ;. J Biol Chem 2001;276:41566-41575.. [3]. 7876261. Structure and function of transcription-repair coupling factor.. I. Structural domains and binding properties.. Selby CP, Sancar A;. J Biol Chem 1995;270:4882-4889.. [4]. 16879646. Recruitment of a novel zinc-bound transcriptional factor by a. bacterial HMGA-type protein is required for regulating multiple. processes in Myxococcus xanthus.. Penalver-Mellado M, Garcia-Heras F, Padmanabhan S, Garcia-Moreno. D, Murillo FJ, Elias-Arnanz M;. Mol Microbiol. 2006;61:910-926.. [5]. 2. TRUNCATED at 1650 bytes (from Pfam)

Date:

2024-08-14

Fpg/Nei family DNA glycosylase similar to Mycobacterium tuberculosis bifunctional DNA-(apurinic or apyrimidinic site) lyase removes damaged bases from DNA, leaving an abasic site, and also probably cleaves the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates

Date:

2022-09-27