Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.76 kDa 
• Atom Count: 6498 
• Modelled Residue Count: 768 
• Deposited Residue Count: 780 
• Unique protein chains: 1

1KIJ

Crystal structure of the 43K ATPase domain of Thermus thermophilus gyrase B in complex with novobiocin

• PDB DOI: 10.2210/pdb1KIJ/pdb

• Classification: ISOMERASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-12-03 Released: 2002-06-03 
• Deposition Author(s): Lamour, V., Hoermann, L., Jeltsch, J.-M., Oudet, P., Moras, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.266 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Literature

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

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

(2002) J Biol Chem 277: 18947-18953

• PubMed: 11850422 
• DOI: 10.1074/jbc.M111740200
• Primary Citation of Related Structures:  
  1KIJ


• PubMed 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.

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Organizational Affiliation: 

Institut de Génétique et de Biologie Moléculaire, CNRS/INSERM/ULP, BP163, 1 rue Laurent Fries, 67404 Illkirch Cedex, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA GYRASE SUBUNIT B	A, B	390	Thermus thermophilus	Mutation(s): 0  EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q5SHZ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHZ4  Go to UniProtKB:  Q5SHZ4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NOV	C [auth A], E [auth B]	NOVOBIOCIN C31 H36 N2 O11 YJQPYGGHQPGBLI-KGSXXDOSSA-N
FMT	D [auth A], F [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.266 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.88	α = 90
b = 125.55	β = 96.36
c = 79.83	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-12-03 
• Released Date: 2002-06-03 
Deposition Author(s): Lamour, V., Hoermann, L., Jeltsch, J.-M., Oudet, P., Moras, D.

Revision History  

• Version 1.0: 2002-06-03
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2016-06-01
  Changes: Source and taxonomy