PDBsum entry: 1gku

Topoisomerase

PDB-id: 1gku

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

1011 a.a. *

Waters ×157

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1gku

Name:

Topoisomerase

Title:

Reverse gyrase from archaeoglobus fulgidus

Structure:

Reverse gyrase. Chain: b. Synonym: top-rg. Engineered: yes. Mutation: yes

Source:

Archaeoglobus fulgidus. Organism_taxid: 224325. Strain: vc-16. Atcc: 49558. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: german collection of microorganisms (dsmz)

UniProt:

O29238 (RGYR_ARCFU)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

1054 a.a.

Struc:

1011 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 21 residue positions (black crosses)

Enzyme class:

E.C.5.99.1.3   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP-dependent breakage, passage and rejoining of double-stranded DNA.

Resolution:

2.70Å

R-factor:

0.226

R-free:

0.295

Authors:

A.C.Rodriguez,D.Stock

Key ref:

A.C.Rodríguez and D.Stock (2002). Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA.. EMBO J, 21, 418-426. [PubMed id: 11823434] [DOI: 10.1093/emboj/21.3.418]

Date:

21-Aug-01

Release date:

11-Feb-02

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1093/emboj/21.3.418

EMBO J 21:418-426 (2002)

PubMed id: 11823434

Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA.

A.C.Rodríguez, D.Stock.

ABSTRACT

Reverse gyrase is the only topoisomerase known to positively supercoil DNA. The protein appears to be unique to hyperthermophiles, where its activity is believed to protect the genome from denaturation. The 120 kDa enzyme is the only member of the type I topoisomerase family that requires ATP, which is bound and hydrolysed by a helicase-like domain. We have determined the crystal structure of reverse gyrase from Archaeoglobus fulgidus in the presence and absence of nucleotide cofactor. The structure provides the first view of an intact supercoiling enzyme, explains mechanistic differences from other type I topoisomerases and suggests a model for how the two domains of the protein cooperate to positively supercoil DNA. Coordinates have been deposited in the Protein Data Bank under accession codes 1GKU and 1GL9.

Selected figure(s)

Figure 2.
Figure 2 Overall structure of reverse gyrase. (A) Stereo view of the molecule. The catalytic Tyr809 of the C-terminal domain is shown in red as a space-filled model, and helicase motif I (residues 78–85) in red ball-and-stick representation. The colouring of the subdomains of reverse gyrase is the same for all figures except Figures 4B and 5. (B) Side view of the molecule shown with a translucent space-filling envelope. Asterisks indicate four structural elements postulated to contact DNA: dark blue, a putative metal-binding site at the extreme N-terminus; light blue, a -hairpin (residues 201–217); green, the 'latch' subdomain H3 (residues 352–427); yellow, a Zn-finger motif (residues 584–601). The conformation of the Zn-finger as shown is uncertain due to poor electron density, and has not been included in the refined model. Maximum dimensions of the molecule are 130 70 50 Å. (C) End-on view of the molecule, with the N-terminal domain towards the front.

Figure 3.
Figure 3 The C-terminal domain of reverse gyrase and its interaction with the N-terminal domain. (A) Superposition of the C-terminal domain with the 67-kDa catalytic fragment of E.coli topoisomerase I (Lima et al., 1994), shown in grey. The position of domains II and III of topoisomerase I correspond to the 'closed' form of the enzyme. A box encloses the region featured in (B). (B) Stereo view of reverse gyrase superimposed with domains II and III of topoisomerase I in the putative 'open' form (Feinberg et al., 1999). The catalytic Tyr in both enzymes is indicated in red space-filling representation. The arrow indicates the putative movement of reverse gyrase subdomains T2 and T3 during strand passage. This movement would be prevented by subdomain H3 in its current position.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 418-426) copyright 2002.

Figures were selected by an automated process.