PDBsum entry 4ddx

Hydrolase

PDB id: 4ddx

Contents

Protein chains

1102 a.a.

Metals

_ZN ×4

PDB id:

4ddx

Name:

Hydrolase

Title:

Thermotoga maritima reverse gyrase, primitive monoclinic form

Structure:

Reverse gyrase. Chain: a, b. Synonym: helicase, topoisomerase. Engineered: yes

Source:

Thermotoga maritima. Organism_taxid: 2336. Gene: rgy, topr, tm_0173. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

4.17Å R-factor: 0.248 R-free: 0.305

Authors:

M.G.Rudolph,D.Klostermeier

Key ref:

M.G.Rudolph et al. (2013). Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling. Nucleic Acids Res, 41, 1058-1070. PubMed id: 23209025

Date:

19-Jan-12 Release date: 26-Dec-12

Protein chains

O51934  (RGYR_THEMA) -  Reverse gyrase from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 1104 a.a.

Struc: 1102 a.a.

Enzyme reactions

• Enzyme class: E.C.5.6.2.- - ?????

Nucleic Acids Res 41:1058-1070 (2013)

PubMed id: 23209025

Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling.

M.G.Rudolph, Y.del Toro Duany, S.P.Jungblut, A.Ganguly, D.Klostermeier.

ABSTRACT

Reverse gyrase is an ATP-dependent topoisomerase that is unique to hyperthermophilic archaea and eubacteria. The only reverse gyrase structure determined to date has revealed the arrangement of the N-terminal helicase domain and the C-terminal topoisomerase domain that intimately cooperate to generate the unique function of positive DNA supercoiling. Although the structure has elicited hypotheses as to how supercoiling may be achieved, it lacks structural elements important for supercoiling and the molecular mechanism of positive supercoiling is still not clear. We present five structures of authentic Thermotoga maritima reverse gyrase that reveal a first view of two interacting zinc fingers that are crucial for positive DNA supercoiling. The so-called latch domain, which connects the helicase and the topoisomerase domains is required for their functional cooperation and presents a novel fold. Structural comparison defines mobile regions in parts of the helicase domain, including a helical insert and the latch that are likely important for DNA binding during catalysis. We show that the latch, the helical insert and the zinc fingers contribute to the binding of DNA to reverse gyrase and are uniquely placed within the reverse gyrase structure to bind and guide DNA during strand passage. A possible mechanism for positive supercoiling by reverse gyrases is presented.