Summary: DNase/tRNase domain of colicin-like bacteriocin
DNase/tRNase domain of colicin-like bacteriocin Provide feedback
Colicin-like bacteriocins are complex structures with an N-terminal beta-barrel translocation domain (PF09000), a long double-alpha-helical receptor-binding domain (PF11570) and this C-terminal RNAse/DNase domain with endonuclease activity. Their competitor bacteriocidal action is by a process that involves binding to a surface receptor, entering the cell, and, finally, killing it. The lethal action of colicin E3 is a specific cleavage in the ribosomal decoding A site. The crystal structure of colicin E3 reveals a Y-shaped molecule with the receptor binding domain forming a 100 Angstrom long stalk and the two globular heads of the translocation domain and this catalytic domain comprising the two arms .
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR024622
This entry represents a C-terminal domain with endonuclease activity found in some colicin/pyocin bacteriocins, including colicin E2, E7, E9 and pyocin S1 and S2. The structure of this domain in colicin E7 has been described as a novel alpha/beta fold containing a Zn2+ ion [PUBMED:10368275].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||endonuclease activity (GO:0004519)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
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Curation and family details
|Number in seed:||57|
|Number in full:||525|
|Average length of the domain:||108.50 aa|
|Average identity of full alignment:||29 %|
|Average coverage of the sequence by the domain:||25.68 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
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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 Colicin-DNase domain has been found. There are 56 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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