{PDOC52014}
{PS52014; SAMD1_WH}
{BEGIN}
***********************************************
* SAMD1-like winged helix (WH) domain profile *
***********************************************

The SAMD1-like  winged  helix  (WH)  domain  forms  a group of WH domains with
shared sequence homology found in the following transcriptional regulators:

 - Animal  SAM  domain-containing  protein  1 (SAMD1) (also named Atherin), an
   unmethylated CGI-binding  protein that cooperates with chromatin regulators
   to modulate the chromatin landscape and down-regulate its target genes [1].
 - Animal  Lysine  Acetyltransferase  6A  (KAT6A),  also  named  MYST3 and MOZ
   Monocytic leukemic   zinc-finger),   a   histone   acetyltransferase   that
   acetylates lysine residues in histone H3 and histone H4 [1].
 - Animal  Lysine  Acetyltransferase  6B  (KAT6B),  also  named MYST4 and MORF
   (Monocytic leukemia   zinc   finger   protein-related  factor),  a  histone
   acetyltransferase which  may  be  involved  in  both  positive and negative
   regulation of transcription.
 - Animal zinc finger MYND-type containing 11 (ZMYND11), a transcriptional co-
   repressor that interacts selectively with histone H3.3.

Within this  group,  the  SAMD1-like  WH  domains  of  KAT6A, -B and SAMD1 are
similar to each other, while the one of ZMYND11 is more distant. The KAT6A, -B
and SAMD1 SAMD1-like WH domain directly recognizes unmethylated CpG-containing
DNA via  simultaneous  interactions  with  both the major and the minor groove
[1,2].

The SAMD1-like  WH  domain has the fold of a winged helix domain that contains
three alpha  helices  at  the  N-terminal  half and two beta strands at the C-
terminal half  (see  <PDB:6LUI>).  Wing-like  loops  between strands beta1 and
beta2 (W1)  and  after  beta2 (W2) are observed. Both the major groove and the
minor groove  of  the CpG-containing DNA are recognized. The C terminal end of
the alpha1  helix  inserts into the CpG-containing major groove. The DNA minor
groove is  contacted  either trough the W1 loop (SAMD1) or through the W2 loop
(KAT6A) [1,2].

The profile we developed covers the entire SAMD1-like WH domain.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: January 2023 / First entry.

[ 1] Stielow B., Zhou Y., Cao Y., Simon C., Pogoda H.-M., Jiang J., Ren Y.,
     Phanor S.K., Rohner I., Nist A., Stiewe T., Hammerschmidt M., Shi Y.,
     Bulyk M.L., Wang Z., Liefke R.
     "The SAM domain-containing protein 1 (SAMD1) acts as a repressive
     chromatin  regulator at unmethylated CpG islands."
     Sci. Adv. 7:0-0(2021).
     PubMed=33980486; DOI=10.1126/sciadv.abf2229
[ 2] Weber L.M., Jia Y., Stielow B., Gisselbrecht S.S., Cao Y., Ren Y.,
     Rohner I., King J., Rothman E., Fischer S., Simon C., Forne I.,
     Nist A., Stiewe T., Bulyk M.L., Wang Z., Liefke R.
     "The histone acetyltransferase KAT6A is recruited to unmethylated CpG
     islands via  a DNA binding winged helix domain."
     Nucleic. Acids. Res. 0:0-0(2022).
     PubMed=36537216; DOI=10.1093/nar/gkac1188

--------------------------------------------------------------------------------
PROSITE is copyrighted by the SIB Swiss Institute of Bioinformatics and
distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives
(CC BY-NC-ND 4.0) License, see https://prosite.expasy.org/prosite_license.html
--------------------------------------------------------------------------------

{END}