Summary: DinB family
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DNA damage-inducible (din) genes in Bacillus subtilis are coordinately regulated and together compose a global regulatory network that has been termed the SOS-like or SOB regulon. This family includes DinB from B. subtilis .
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This tab holds annotation information from the InterPro database.
InterPro entry IPR007837This entry represents the DinB family, and includes DinB from Bacillus subtilis. DNA damage-inducible genes (dinA, dinB, and dinC) in Bacillus subtilis are coordinately regulated and together compose a global regulatory network that has been termed the SOS-like or SOB regulon [PUBMED:1847907].
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This superfamily are thought to be metalloenzymes. They possess a four helical bundle core structure with a beta hairpin. Members of the superfamily have a predicted active site composed of three histidines that chelate Nickel or Zinc. In some cases these histidines are replaced with Aspartate or Glutamate. Mostly they form a dimeric structure. The dinB gene is one of the DNA-damage-induced genes and the corresponding protein, DinB, is the founding member of the clan. The protein contains a four-helix up-down-down-up bundle that has previously been described in the literature in three disparate proteins: the enzyme MDMPI (mycothiol-dependent maleylpyruvate isomerase), YfiT and TTHA0303, a member of a small DUF (domain of unknown function). Most (but not all) clan members seem to have the ability to coordinate a metal ion using a conserved histidine-triad motif. The proteins that share the fold exhibit four different quaternary structures: monomeric and three different dimeric forms .
The clan contains the following 8 members:DinB DinB_2 DUF1569 DUF1572 DUF1706 DUF1993 DUF664 MDMPI_N
We make a range of alignments for each Pfam-A family:
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Curation and family details
|Number in seed:||14|
|Number in full:||1291|
|Average length of the domain:||161.30 aa|
|Average identity of full alignment:||18 %|
|Average coverage of the sequence by the domain:||97.05 %|
|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:||7|
|Download:||download the raw HMM for this family|
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We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 DinB domain has been found. There are 11 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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