{PDOC52036}
{PS52036; ZF_RG_N}
{PS52037; ZF_RG_C}
{BEGIN}
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* Zinc finger reverse gyrase (RG) N-terminal- and C-terminal-type profiles *
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Regulation of  DNA  topology  is  central  to  a multitude of cellular events,
including gene  expression,  DNA  replication,  recombination  and repair. DNA
topoisomerases inter-convert  topoisomers  by introducing or removing positive
or negative  supercoils. Reverse gyrase (RG) is an ATP-dependent topoisomerase
that is  only  found  in  archaeal  and  bacterial hyperthermophiles (above 80
degrees C)  and thermophiles (65-80 degrees C). It can protect DNA from damage
at high  temperatures as a heat-protective DNA chaperone or DNA renaturase and
it is  also  involved  in  protecting DNA against physical or chemical damage.
RGs share  a modular structure with an N-terminal cysteine-rich region (a zinc
finger) preceding   a  helicase  domain  that  is  followed  by  a  C-terminal
topoisomerase domain. The helicase domain is subdivided into H1 and H2 domains
that are  flexibly  linked.  Some  RG  topoisomerase  domains  also  include a
cysteine-rich region  that has been proposed to form a second zinc finger. The
two zinc-finger  motifs  are  found to be important to the structure stability
maintenance of  RG  at  high  temperature.  The  N-terminal zinc finger firmly
attaches the  H1  domain  to  the  topoisomerase  domain and may contribute to
double-strand DNA  (dsDNA)  binding.  The  second  zinc  finger locates to the
topoisomerase domain at a position close to the single-strand DNA-binding site
[1,2].

The N-terminal cysteine-rich region folds into a compact domain that harbors a
Gag-knuckle zinc  finger.  A  beta-hairpin  called  a zinc-knuckle carries two
cysteine residues at its tip and two more zinc ligands are provided by a short
alpha-helix or  loop region. The C-terminal cysteine-rich region in RG forms a
zinc finger  of  the ribbon type with two zinc knuckles clamping onto the zinc
ion. The  zinc  knuckles  are  joined  by  an additional beta-strand to form a
three-stranded anti-parallel  beta-sheet.  The  zinc  ribbon in RG is inserted
into the  Toprim  domain (see <PDOC50880>) at the base of the DNA-binding site
and protrudes  from  the  surface of the topoisomerase domain (see <PDB:4DDX>)
[1].

The profiles  we  developed  cover  respectively the entire RG N-terminal- and
C-terminal-type zinc fingers.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.

-Last update: September 2023 / First entry.

[ 1] Rudolph M.G., del Toro Duany Y., Jungblut S.P., Ganguly A.,
     Klostermeier D.
     "Crystal structures of Thermotoga maritima reverse gyrase: inferences
     for the  mechanism of positive DNA supercoiling."
     Nucleic. Acids. Res. 41:1058-1070(2013).
     PubMed=23209025; DOI=10.1093/nar/gks1073
[ 2] Li J., Liu J., Zhou J., Xiang H.
     "Functional evaluation of four putative DNA-binding regions in
     Thermoanaerobacter  tengcongensis reverse gyrase."
     Extremophiles 15:281-291(2011).
     PubMed=21318561; DOI=10.1007/s00792-011-0356-5

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