9FDD

The crystal structure of full length tetramer CysB from Klebsiella aerogenes in complex with N-acetylserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.180 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The Structure of the LysR-type Transcriptional Regulator, CysB, Bound to the Inducer, N-acetylserine.

Verschueren, K.H.G.Dodson, E.J.Wilkinson, A.J.

(2024) Eur Biophys J 53: 311-326

  • DOI: https://doi.org/10.1007/s00249-024-01716-w
  • Primary Citation of Related Structures:  
    9F14, 9FDD

  • PubMed Abstract: 

    In Escherichia coli and Salmonella typhimurium, cysteine biosynthesis requires the products of 20 or more cys genes co-ordinately regulated by CysB. Under conditions of sulphur limitation and in the presence of the inducer, N-acetylserine, CysB binds to cys promoters and activates the transcription of the downstream coding sequences. CysB is a homotetramer, comprising an N-terminal DNA binding domain (DBD) and a C-terminal effector binding domain (EBD). The crystal structure of a dimeric EBD fragment of CysB from Klebsiella aerogenes revealed a protein fold similar to that seen in Lac repressor but with a different symmetry in the dimer so that the mode of DNA binding was not apparent. To elucidate the subunit arrangement in the tetramer, we determined the crystal structure of intact CysB in complex with N-acetylserine. The tetramer has two subunit types that differ in the juxtaposition of their winged helix-turn-helix DNA binding domains with respect to the effector binding domain. In the assembly, the four EBDs form a core with the DNA binding domains arranged in pairs on the surface. N-acetylserine makes extensive polar interactions in an enclosed binding site, and its binding is accompanied by substantial conformational rearrangements of surrounding residues that are propagated to the protein surface where they appear to alter the arrangement of the DNA binding domains. The results are (i) discussed in relation to the extensive mutational data available for CysB and (ii) used to propose a structural mechanism of N-acetylserine induced CysB activation.


  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York, YO10 5DD, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HTH-type transcriptional regulator CysB
A, B, C, D, E
A, B, C, D, E, F, G, H
324KlebsiellaMutation(s): 0 
Gene Names: cysB
UniProt
Find proteins for P45600 (Klebsiella pneumoniae)
Explore P45600 
Go to UniProtKB:  P45600
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45600
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.180 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.436α = 90
b = 187.436β = 90
c = 224.662γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
REFMACrefinement
HKL-3000data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBO4808

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references
  • Version 1.2: 2024-08-28
    Changes: Database references