{PDOC51341}
{PS51341; ZF_LTAG_D1}
{BEGIN}
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* Zinc finger large T-antigen (T-ag) D1-type profile *
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The group  of  polyomaviruses is formed by the homonymous murine virus (Py) as
well as  other  representative  members such as the simian virus 40 (SV40) and
the human BK and JC viruses [1]. Their large T antigen (T-ag) protein binds to
and activates  DNA  replication  from  the  origine  of DNA replication (ori).
Insofar as  is  known,  the T-ag binds to the origin first as a monomer to its
pentanucleotide recognition element. The monomers are then thought to assemble
into hexamers and double hexamers, which constitute the form that is active in
initiation of  DNA  replication.  When  bound to the ori, T-ag double hexamers
encircle DNA  [2]. T-ag is a multidomain protein that contains an N-terminal J
domain (see   <PDOC00553>),   a   central  origin-binding  domain  (OBD)  (see
<PDOC51287>), and a C-terminal superfamily 3 helicase domain (see <PDOC51206>)
[3]. The  helicase domain actually contains three distinct structural domains:
D1 (domain  1),  D2  and  D3  (see  <PDB:1N25>).  D1 is the Zn domain at the N
terminus and   contains   five  alpha-helices  (alpha1-alpha5).  The  Zn  atom
coordinated by  a  Zn motif is important in holding alpha3 (alpha-helix 3) and
alpha4 together,  which  in  turn provide an anchor for alpha1 and alpha2. The
beginning of  alpha5  packs  with  alpha1 and alpha2 of D1, but its C terminus
extends to  alpha6  of  D3.  The  D2  domain contains three conserved helicase
motifs related to SF3 helicases, namely the modified version of Walker A and B
motifs and  motif  C.  D2  folds  into  a  core  beta-sheet consisting of five
parallel beta-strands  sandwiched  by  alpha-helices. The third domain, D3, is
all alpha-helical  Its  seven alpha-helices originate from both the N-terminal
region (alpha6-alpha8)  and the C terminus (alpha13-alpha16), with D2 inserted
between [4].

The Zn  motif  of  T-Ag was proposed to form a canonical zinc-finger structure
for DNA binding. However, the Zn domain (D1) has a globular fold stabilized by
the coordination  of  a  Zn  atom through the Zn motif, and no classical zinc-
finger structure  specialized  for DNA binding is present. The Zn motif is not
directly involved  in binding DNA but is instead important for stabilizing the
Zn-domain structure [4].

The profile we developed covers the entire T-ag D1-type zinc finger.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: November 2007 / First entry.

[ 1] Iacoangeli A., Melucci-Vigo G., Risuleo G., Santi E.
     "Role of mouse polyomavirus late region in the control of viral DNA
     replication: a review."
     Biochimie 77:780-786(1995).
     PubMed=8824775
[ 2] Bochkareva E., Martynowski D., Seitova A., Bochkarev A.
     "Structure of the origin-binding domain of simian virus 40 large T
     antigen bound to DNA."
     EMBO J. 25:5961-5969(2006).
     PubMed=17139255; DOI=10.1038/sj.emboj.7601452
[ 3] Meinke G., Bullock P.A., Bohm A.
     "Crystal structure of the simian virus 40 large T-antigen
     origin-binding domain."
     J. Virol. 80:4304-4312(2006).
     PubMed=16611889; DOI=10.1128/JVI.80.9.4304-4312.2006
[ 4] Li D., Zhao R., Lilyestrom W., Gai D., Zhang R., DeCaprio J.A.,
     Fanning E., Jochimiak A., Szakonyi G., Chen X.S.
     "Structure of the replicative helicase of the oncoprotein SV40 large
     tumour antigen."
     Nature 423:512-518(2003).
     PubMed=12774115; DOI=10.1038/nature01691

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