2ZJT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 

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This is version 1.2 of the entry. See complete history


Literature

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

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.

(2009) Nucleic Acids Res 37: 5908-5916

  • DOI: 10.1093/nar/gkp586
  • Primary Citation of Related Structures:  
    2ZJT

  • 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 ...

    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.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BA, B247Mycobacterium tuberculosisMutation(s): 0 
Gene Names: gyrB
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P9WG45 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WG45 
Go to UniProtKB:  P9WG45
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.831α = 90
b = 52.763β = 90
c = 192.579γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-02-12
    Changes: Database references