PROSITE documentation PDOC00044

{PDOC00044}
{PS00045; HISTONE_LIKE}
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* Bacterial histone-like DNA-binding proteins signature *
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Bacteria  synthesize  a set  of  small,  usually  basic proteins  of  about 90
residues that bind DNA and are known as histone-like proteins [1,2]. The exact
function of  these proteins is not yet clear but they  are capable of wrapping
DNA and   stabilizing   it   from  denaturation  under  extreme  environmental
conditions.  The sequence of a number of different types  of these proteins is
known:

 - The HU proteins, which, in Escherichia coli, are a dimer of closely related
   alpha and  beta  chains  and,  in other bacteria, can be dimer of identical
   chains. HU-type  proteins  have  been  found  in  a  variety of eubacteria,
   cyanobacteria and archaebacteria, and are also encoded  in  the chloroplast
   genome of some algae [3].
 - The integration host factor (IHF), a dimer of  closely related chains which
   seem to  function  in genetic recombination as well as in translational and
   transcriptional control [4] in enterobacteria.
 - The bacteriophage sp01 transcription factor 1 (TF1) which selectively binds
   to and inhibits  the  transcription  of hydroxymethyluracil-containing DNA,
   such as sp01 DNA, by RNA polymerase in vitro.
 - The African Swine fever virus protein A104R (or LMW5-AR) [5].

As a signature pattern for  this family of proteins,  we use a  twenty residue
sequence which includes three perfectly conserved positions.  According to the
tertiary structure  of  one  of these proteins [6], this pattern spans exactly
the first half of the flexible DNA-binding arm.

-Consensus pattern: [GSK]-F-x(2)-[LIVMF]-x(4)-[RKEQA]-x(2)-[RST]-x(1,2)-[GA]-
                    x-[KN]-P-x-[TN]
-Sequences known to belong to this class detected by the pattern: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: December 2004 / Pattern and text revised.

[ 1] Drlica K., Rouviere-Yaniv J.
     "Histonelike proteins of bacteria."
     Microbiol. Rev. 51:301-319(1987).
     PubMed=3118156
[ 2] Pettijohn D.E.
     "Histone-like proteins and bacterial chromosome structure."
     J. Biol. Chem. 263:12793-12796(1988).
     PubMed=3047111
[ 3] Wang S.L., Liu X.-Q.
     "The plastid genome of Cryptomonas phi encodes an hsp70-like protein,
     a histone-like protein, and an acyl carrier protein."
     Proc. Natl. Acad. Sci. U.S.A. 88:10783-10787(1991).
     PubMed=1961745
[ 4] Friedman D.I.
     "Integration host factor: a protein for all reasons."
     Cell 55:545-554(1988).
     PubMed=2972385
[ 5] Neilan J.G., Lu Z., Kutish G.F., Sussman M.D., Roberts P.C.,
     Yozawa T., Rock D.L.
     "An African swine fever virus gene with similarity to bacterial DNA
     binding proteins, bacterial integration host factors, and the Bacillus
     phage SPO1 transcription factor, TF1."
     Nucleic Acids Res. 21:1496-1496(1993).
     PubMed=8464748
[ 6] Tanaka I., Appelt K., Dijk J., White S.W., Wilson K.S.
     "3-A resolution structure of a protein with histone-like properties in
     prokaryotes."
     Nature 310:376-381(1984).
     PubMed=6540370

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