PDBsum entry: 1kij

Isomerase

PDB id: 1kij

Contents

Protein chains

384 a.a. *

Ligands

NOV ×2

FMT ×2

Waters ×468

* Residue conservation analysis

PDB id:

1kij

Name:

Isomerase

Title:

Crystal structure of the 43k atpase domain of thermus thermo gyrase b in complex with novobiocin

Structure:

DNA gyrase subunit b. Chain: a, b. Fragment: 43k domain. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.206 R-free: 0.266

Authors:

V.Lamour,L.Hoermann,J.-M.Jeltsch,P.Oudet,D.Moras

Key ref:

V.Lamour et al. (2002). An open conformation of the Thermus thermophilus gyrase B ATP-binding domain. J Biol Chem, 277, 18947-18953. PubMed id: 11850422 DOI: 10.1074/jbc.M111740200

Date:

03-Dec-01 Release date: 03-Jun-02

Protein chains

Q9LCX5  (Q9LCX5_THETH) -  DNA gyrase subunit B

Seq: 634 a.a.

Struc: 384 a.a.

Enzyme reactions

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

 Gene Ontology (GO) functional annotation 

• Cellular component: chromosome (1 term)
• Biological process: DNA topological change (1 term)
• Biochemical function: DNA binding (3 terms)

DOI no: 10.1074/jbc.M111740200

J Biol Chem 277:18947-18953 (2002)

PubMed id: 11850422

An open conformation of the Thermus thermophilus gyrase B ATP-binding domain.

V.Lamour, L.Hoermann, J.M.Jeltsch, P.Oudet, D.Moras.

ABSTRACT

DNA gyrase forms an A(2)B(2) tetramer involved in DNA replication, repair, recombination, and transcription in which the B subunit catalyzes ATP hydrolysis. The Thermus thermophilus and Escherichia coli gyrases are homologues and present the same catalytic activity. When compared with that of the E. coli 43K-5'-adenylyl-beta,gamma-imidodiphosphate complex, the crystal structure of Gyrase B 43K ATPase domain in complex with novobiocin, one of the most potent inhibitors of gyrase shows large conformational changes of the subdomains within the dimer. The stabilization of loop 98-118 closing the active site through dimeric contacts and interaction with domain 2 allows to observe novobiocin-protein interactions that could not be seen in the 24K-inhibitor complexes. Furthermore, this loop adopts a position which defines an "open" conformation of the active site in absence of ATP, in contrast with the "closed" conformation adopted upon ATP binding. All together, these results indicate how the subdomains may propagate conformational changes from the active site and provide crucial information for the design of more specific inhibitors.

Selected figure(s)

Figure 5.
Fig. 5. Novobiocin binding. The novobiocin molecule (in blue) lies at the entry of the ATP-binding site with electronic density (final map 2F[o] F[c], 1.3 ) shown in orange. Most of the contacts with the pocket are the same as the ones previously observed with the 24K domain. Due to the dimer formation and the resulting stabilization of loop 98-118 (shown in red), additional residues (in yellow) contribute to the hydrophobic region of the pocket, among them is Ile^10 from the N-terminal arm of the other monomer (in purple). There is also one additional strong H-bond with Asp80 (a Gly in E. coli) upstream loop 83-89 (in green).

Figure 6.
Fig. 6. Open and closed conformation of the active site. In the closed conformation (in yellow), the loop 98-118 is tightened around the ATP molecule (ADPPNP in red) which -phosphate is contacted by domain 2 residues Lys337 and Gln335. Lys102 (E.c. 103) and Lys109 (E.c. 110) implicated in the catalysis as well as Tyr108 (E.c. 109) binding the ATP adenine ring undergo large movement (respectively, blue and red arrows) in the absence of ATP. The novobiocin molecule (in sky blue) blocks the open conformation of the active site (in blue) which might be one conformation of the active site after ATP hydrolysis. E.c., E. coli.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 18947-18953) copyright 2002.

Figures were selected by the author.