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9  structures 62  species 3  interactions 512  sequences 13  architectures

Family: Endotoxin_C (PF03944)

Summary: delta endotoxin

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Delta endotoxin Edit Wikipedia article

delta endotoxin, N-terminal domain
PDB 1ji6 EBI.jpg
crystal structure of the insecticidal bacterial del endotoxin Cry3Bb1 bacillus thuringiensis
Identifiers
Symbol Endotoxin_N
Pfam PF03945
InterPro IPR005639
SCOP 1dlc
SUPERFAMILY 1dlc
TCDB 1.C.2
delta endotoxin
PDB 1dlc EBI.jpg
Structure of insecticidal delta-endotoxin from Bacillus thuringiensis.[1]
Identifiers
Symbol Endotoxin_M
Pfam PF00555
InterPro IPR015790
SCOP 1dlc
SUPERFAMILY 1dlc
TCDB 1.C.2
OPM superfamily 95
OPM protein 1w99
Bacillus thuringiensis delta-Endotoxin, middle domain
PDB 1i5p EBI.jpg
insecticidal crystal protein cry2aa
Identifiers
Symbol Endotoxin_mid
Pfam PF09131
InterPro IPR015214
SCOP 1i5p
SUPERFAMILY 1i5p
delta endotoxin
PDB 1i5p EBI.jpg
insecticidal crystal protein cry2aa
Identifiers
Symbol Endotoxin_C
Pfam PF03944
Pfam clan CL0202
InterPro IPR005638
SCOP 1dlc
SUPERFAMILY 1dlc
TCDB 1.C.2

Delta endotoxins (δ-endotoxins, also called Cry and Cyt toxins) are pore-forming toxins produced by Bacillus thuringiensis species of bacteria. They are useful for their insecticidal action.

During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins, they are activated by proteolytic cleavage. The N-terminus is cleaved in all of the proteins and a C-terminal extension is cleaved in some members. Once activated, the endotoxin binds to the gut epithelium and causes cell lysis by the formation of cation-selective channels, which leads to death. The activated region of the delta toxin is composed of three distinct structural domains: an N-terminal helical bundle domain (IPR005639) involved in membrane insertion and pore formation; a beta-sheet central domain involved in receptor binding; and a C-terminal beta-sandwich domain (IPR005638) that interacts with the N-terminal domain to form a channel.[2][3][4][5]

References

  1. ^ Li JD, Carroll J, Ellar DJ (October 1991). "Crystal structure of insecticidal delta-endotoxin from Bacillus thuringiensis at 2.5 A resolution". Nature 353 (6347): 815–21. doi:10.1038/353815a0. PMID 1658659. 
  2. ^ Cygler M, Borisova S, Grochulski P, Masson L, Pusztai-carey M, Schwartz JL, Brousseau R (1995). "Bacillus thuringiensis CryIA(a) insecticidal toxin: crystal structure and channel formation". J. Mol. Biol. 254 (3): 447–464. doi:10.1006/jmbi.1995.0630. PMID 7490762. 
  3. ^ Ghosh D, Pangborn W, Galitsky N, Cody V, Wojtczak A, Luft JR, English L (2001). "Structure of the insecticidal bacterial delta-endotoxinCry3Bb1 of Bacillus thuringiensis". Acta Crystallogr. D 57 (8): 1101–1109. doi:10.1107/S0907444901008186. PMID 11468393. 
  4. ^ Grochulski P, Masson L, Borisova S, Pusztai-Carey M, Schwartz JL, Brousseau R, Cygler M (December 1995). "Bacillus thuringiensis CryIA(a) insecticidal toxin: crystal structure and channel formation". J. Mol. Biol. 254 (3): 447–64. doi:10.1006/jmbi.1995.0630. PMID 7490762. 
  5. ^ Galitsky N, Cody V, Wojtczak A, Ghosh D, Luft JR, Pangborn W, English L (August 2001). "Structure of the insecticidal bacterial delta-endotoxin Cry3Bb1 of Bacillus thuringiensis". Acta Crystallogr. D Biol. Crystallogr. 57 (Pt 8): 1101–9. doi:10.1107/S0907444901008186. PMID 11468393. 

Further reading

This article incorporates text from the public domain Pfam and InterPro IPR015790

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members. Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death. This activated region of the delta endotoxin is composed of three structural domains. The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding.

Literature references

  1. Li J, Carroll J, Ellar DJ; , Nature 1991;353:815-821.: Crystal structure of insecticidal delta-endotoxin from Bacillus thuringiensis at 2.5 angstroms resolution. PUBMED:1658659 EPMC:1658659

  2. Schnepf E, Crickmore N, Van Rie J, Lereclus D, Baum J, Feitelson J, Zeigler DR, Dean DH; , Microbiol Mol Biol Rev 1998;62:775-806.: Bacillus thuringiensis and its pesticidal crystal proteins. PUBMED:9729609 EPMC:9729609


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005638

This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins, they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C-terminal extension is cleaved in some members. Once activated, the endotoxin binds to the gut epithelium and causes cell lysis by the formation of cation-selective channels, which leads to death. The activated region of the delta toxin is composed of three distinct structural domains: an N-terminal helical bundle domain (INTERPRO) involved in membrane insertion and pore formation; a beta-sheet central domain (INTERPRO) involved in receptor binding; and a C-terminal beta-sandwich domain that interacts with the N-terminal domain to form a channel [PUBMED:7490762, PUBMED:11468393]. This entry represents the conserved C-terminal domain.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan GBD (CL0202), which has the following description:

This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].

The clan contains the following 27 members:

Allantoicase APC10 Bac_rhamnosid_N BetaGal_dom4_5 CBM_11 CBM_15 CBM_17_28 CBM_4_9 CBM_6 CIA30 Cleaved_Adhesin DUF642 Endotoxin_C Ephrin_lbd F5_F8_type_C FBA Glyco_hydro_2_N Laminin_N Lyase_N MAM Muskelin_N P_proprotein PA-IL PepX_C PITH Sad1_UNC XRCC1_N

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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Full
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Representative proteomes NCBI
(538)
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(2)
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RP35
(4)
RP55
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RP75
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  Seed
(80)
Full
(512)
Representative proteomes NCBI
(538)
Meta
(2)
RP15
(2)
RP35
(4)
RP55
(4)
RP75
(5)
Alignment:
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  Seed
(80)
Full
(512)
Representative proteomes NCBI
(538)
Meta
(2)
RP15
(2)
RP35
(4)
RP55
(4)
RP75
(5)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: Arne Eloffson
Previous IDs: endotoxin_C;
Type: Domain
Author: Bateman A, de Maagd R
Number in seed: 80
Number in full: 512
Average length of the domain: 134.80 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 15.34 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.0 21.0
Trusted cut-off 21.4 21.4
Noise cut-off 20.7 20.7
Model length: 143
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

Endotoxin_mid Endotoxin_M Endotoxin_N

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Endotoxin_C domain has been found. There are 9 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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