2ZJT

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

Summary for 2ZJT

• Entry DOI: 10.2210/pdb2zjt/pdb
• Related: 1AB4 1BGW 1BJT 1EI1 1SUU 2NOV 2RGR
• Descriptor: DNA gyrase subunit B (1 entity in total)
• Functional Keywords: dna gyrase, gyrb-ctd, toprim, tail, dna topoisomerase ii, g-segment, t-segment, atp-binding, nucleotide-binding, isomerase
• Biological source: Mycobacterium tuberculosis
• Cellular location: Cytoplasm (Potential): P0C5C5
• Total number of polymer chains: 2
• Total formula weight: 55874.02

Authors

Fu, G.S.,Zhu, D.Y.,Hu, Y.L.,Wang, D.C. (deposition date: 2008-03-10, release date: 2009-03-10, Last modification date: 2024-03-13)

Primary citation

Fu, G.S.,Wu, J.J.,Liu, W.,Zhu, D.Y.,Hu, Y.L.,Deng, J.,Zhang, X.E.,Bi, L.J.,Wang, D.C.
Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation
Nucleic Acids Res., 37:5908-5916, 2009

PubMed 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.

PubMed: 19596812
DOI: 10.1093/nar/gkp586

Experimental method

X-RAY DIFFRACTION (2.8 Å)