looped-hinge helix DNA binding domain, AbrB family; This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609. [Regulatory functions, DNA interactions]

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                 ....*....|....*....|....*....|....*....|...
gi 15609732    3 TTIDVAGRLVIPKRIRERLGLRGNDQVEITE-RDGRIEIEPAP 44
Cdd:TIGR01439  1 VTVDKKGQIVIPKEIREKLGLKEGDRLEVIRvEDGEIILRPKR 43

Antidote-toxin recognition MazE, bacterial antitoxin; AbrB-like is a family of small proteins that operate in conjunction with a cognate toxin molecule. The commonly attributed role of toxin-antitoxin systems is to maintain low-copy number plasmids from one generation to the next. Such gene-pairs are also found on chromosomes and to be associated with a number of biological functions such as: reduction of protein synthesis, gene regulation and retardation of cell growth under nutritional stress. This family includes proteins from a number of different pairings, eg MazE, AbrB, VapB, PhoU, PemI-like and SpoVT. MazE is the antidote to the toxin MazF of E. coli. MazE-MazF in E. coli is a regulated prokaryotic chromosomal addiction module. MazE antidote is degraded by the ClpPA protease of the bacterial proteasome. MazE-MazF is thought to play a role in programmed cell death when cells suffer nutrient deprivation, and MazE-MazF modules have also been implicated in the bacteriostatic effects of other addiction modules.

                         10        20        30
                 ....*....|....*....|....*....|....
gi 15609732    9 GRLVIPKRIRERLGLRGNDQVEITERDGRIEIEP 42
Cdd:pfam04014  7 GAVRIPKEVRKALGIKEGDEVELEVDGDKIILKP 40

looped-hinge helix DNA binding domain, AbrB family; This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609. [Regulatory functions, DNA interactions]

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 15609732    3 TTIDVAGRLVIPKRIRERLGLRGNDQVEITE-RDGRIEIEPAP 44
Cdd:TIGR01439  1 VTVDKKGQIVIPKEIREKLGLKEGDRLEVIRvEDGEIILRPKR 43

SpoVT / AbrB like domain; This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. AbrB is thought to interact directly with the transcription initiation regions of genes under its control. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator. DNA-binding activity in this AbrB homologue requires hexamerisation. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 15609732     3 TTIDVAGRLVIPKRIRERLGLRGNDQVEITERDGRIEIEPAP 44
Cdd:smart00966  1 VKVGNSGQVTIPKEVREKLGIKEGDEVELEVDGDGIILEPVK 42