{PDOC51253}
{PS51253; HTH_CENPB}
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* CENPB-type HTH domain profile *
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The  CENPB-type  HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of
about  70-75  amino  acids,  present  in  eukaryotic  centromere  proteins and
transposases.  The  domain  is  named  after  the  mammalian  major centromere
autoantigen  B  or  centromere  protein  B  (CENP-B),  which  is a fundamental
centromere  component  of  chromosomes.  The N-terminus of CENP-B contains two
DNA-binding  HTH  domains,  which  bind  to adjacent major grooves of DNA. The
N-terminus  of CENP-B is formed by a psq-type HTH domain (see <PDOC50960>) and
C-terminal  to  this  domain  lies  the  CENPB-type  HTH domain. These two HTH
domains together bind specifically to a 17-base-pair sequence, the CENP-B box,
which occurs in alpha-satellite DNA in human centromeres [1].

The  structure of the CENPB-type HTH domain is composed of three alpha-helices
(see  <PDB:1HLV>).  The second and third helices connected via a turn comprise
the  helix-turn-helix  motif.  Helix  3  is termed the recognition helix as it
binds  the  DNA  major  groove,  like  in  other  HTHs.  In CENP-B this domain
recognizes  site  3  of  the CENP-B box, while the preceding psq-type HTH (see
<PDOC50960>)  binds  site  1  of  the CENP-B box, and a connecting linker loop
binds in the minor groove of DNA and recognizes site 2 [2].

Some proteins known to contain a CENPB-type HTH domain:

 - Mammalian centromere protein B (CENP-B), associated with the centromere and
   specifically binding DNA to the CENP-B box.
 - Mammalian jerky protein, involved in epileptic seizures in mice.
 - Mammalian Pogo transposases.
 - Fission  yeast  ARS-binding  protein  1  (abp1) and CENP-B homolog proteins
   (CBHP-1 and 2), which are centromere proteins.
 - Candida albicans protein PDC2.
 - Fungal transposases.

The  profile  we  developed covers the entire CENPB-type HTH domain, including
the N-terminal linker loop.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: September 2006 / First entry.

[ 1] Tanaka Y., Tachiwana H., Yoda K., Masumoto H., Okazaki T.,
     Kurumizaka H., Yokoyama S.
     "Human centromere protein B induces translational positioning of
     nucleosomes on alpha-satellite sequences."
     J. Biol. Chem. 280:41609-41618(2005).
     PubMed=16183641; DOI=10.1074/jbc.M509666200
[ 2] Tanaka Y., Nureki O., Kurumizaka H., Fukai S., Kawaguchi S., Ikuta M.,
     Iwahara J., Okazaki T., Yokoyama S.
     "Crystal structure of the CENP-B protein-DNA complex: the DNA-binding
     domains of CENP-B induce kinks in the CENP-B box DNA."
     EMBO J. 20:6612-6618(2001).
     PubMed=11726497; DOI=10.1093/emboj/20.23.6612

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