PDBsum entry: 1gl9

Topoisomerase

PDB id: 1gl9

Contents

Protein chains

1020 a.a. *

Ligands

ANP ×2

Metals

_MG ×2

* Residue conservation analysis

PDB id:

1gl9

Name:

Topoisomerase

Title:

Archaeoglobus fulgidus reverse gyrase complexed with adpnp

Structure:

Reverse gyrase. Chain: b, c. Synonym: top-rg. Engineered: yes. Mutation: yes. Other_details: adenylylimidodiphosphate (adpnp)

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)

Resolution:

3.20Å R-factor: 0.256 R-free: 0.332

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:

30-Aug-01 Release date: 11-Feb-02

Protein chains

O29238  (RGYR_ARCFU) -  Reverse gyrase

Seq: 1054 a.a.

Struc: 1020 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H₂O = ADP + phosphate

ATP + H(2)O = ADP (Bound ligand (Het Group name = ANP) matches with 81.00% similarity) + phosphate

• Enzyme class 3: E.C.5.99.1.3 - Dna topoisomerase (ATP-hydrolyzing).
• Reaction: ATP-dependent breakage, passage and rejoining of double-stranded DNA.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: chromosome (1 term)
• Biological process: DNA metabolic process (3 terms)
• Biochemical function: nucleotide binding (12 terms)

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.