PDBsum entry: 2zjt

Isomerase

PDB id: 2zjt

Contents

Protein chains

185 a.a. *

* Residue conservation analysis

PDB id:

2zjt

Name:

Isomerase

Title:

Crystal structure of DNA gyrase b' domain sheds lights on the mechanism for t-segment navigation

Structure:

DNA gyrase subunit b. Chain: a, b. Fragment: c-terminal domain. Engineered: yes

Source:

Mycobacterium tuberculosis. Organism_taxid: 1773. Strain: h37rv. Gene: gyrb. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.244 R-free: 0.280

Authors:

G.S.Fu,D.Y.Zhu,Y.L.Hu,D.C.Wang

Key ref:

G.Fu et al. (2009). Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation. Nucleic Acids Res, 37, 5908-5916. PubMed id: 19596812 DOI: 10.1093/nar/gkp586

Date:

10-Mar-08 Release date: 10-Mar-09

Protein chains

P0C5C5  (GYRB_MYCTU) -  DNA gyrase subunit B

Seq: 675 a.a.

Struc: 185 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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: 10.1093/nar/gkp586

Nucleic Acids Res 37:5908-5916 (2009)

PubMed id: 19596812

Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation.

G.Fu, J.Wu, W.Liu, D.Zhu, Y.Hu, J.Deng, X.E.Zhang, L.Bi, D.C.Wang.

ABSTRACT

DNA gyrase is an indispensible marvelous molecular machine in manipulating the DNA topology for the prokaryotes. In the 'two-gate' mechanism of DNA topoisomerase, T-segment navigation from N- to DNA-gate is a critical step, but the structural basis supporting this scheme is unclear. The crystal structure of DNA gyrase B' subfragment from Mycobacterium tuberculosis reveals an intrinsic homodimer. The two subunits, each consisting of a Tail and a Toprim domain, are tightly packed one another to form a 'crab-like' organization never observed previously from yeast topo II. Structural comparisons show two orientational alterations of the Tail domain, which may be dominated by a 43-residue peptide at the B' module C-terminus. A highly conserved pentapeptide mediates large-scale intrasubunit conformational change as a hinge point. Mutational studies highlight the significant roles of a negatively charge cluster on a groove at dimer interface. On the basis of structural analysis and mutation experiments, a sluice-like model for T-segment transport is proposed.