PROSITE documentation PDOC52036
Zinc finger reverse gyrase (RG) N-terminal- and C-terminal-type profiles


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 β-hairpin called a zinc-knuckle carries two cysteine residues at its tip and two more zinc ligands are provided by a short α-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 β-strand to form a three-stranded anti-parallel β-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.

Last update:

September 2023 / First entry.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

ZF_RG_C, PS52037; Zinc finger reverse gyrase C-terminal-type profile  (MATRIX)

ZF_RG_N, PS52036; Zinc finger reverse gyrase N-terminal-type profile  (MATRIX)


1AuthorsRudolph M.G. del Toro Duany Y. Jungblut S.P. Ganguly A. Klostermeier D.
TitleCrystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling.
SourceNucleic. Acids. Res. 41:1058-1070(2013).
PubMed ID23209025

2AuthorsLi J. Liu J. Zhou J. Xiang H.
TitleFunctional evaluation of four putative DNA-binding regions in Thermoanaerobacter tengcongensis reverse gyrase.
SourceExtremophiles 15:281-291(2011).
PubMed ID21318561

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