4NHJ

Crystal structure of Klebsiella pneumoniae RstA DNA-binding domain in complex with RstA box


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural dynamics of the two-component response regulator RstA in recognition of promoter DNA element.

Li, Y.C.Chang, C.K.Chang, C.F.Cheng, Y.H.Fang, P.J.Yu, T.Chen, S.C.Li, Y.C.Hsiao, C.D.Huang, T.H.

(2014) Nucleic Acids Res 42: 8777-8788

  • DOI: 10.1093/nar/gku572
  • Primary Citation of Related Structures:  
    4NHJ, 4NIC, 2MLK

  • PubMed Abstract: 
  • The RstA/RstB system is a bacterial two-component regulatory system consisting of the membrane sensor, RstB and its cognate response regulator (RR) RstA. The RstA of Klebsiella pneumoniae (kpRstA) consists of an N-terminal receiver domain (RD, residu ...

    The RstA/RstB system is a bacterial two-component regulatory system consisting of the membrane sensor, RstB and its cognate response regulator (RR) RstA. The RstA of Klebsiella pneumoniae (kpRstA) consists of an N-terminal receiver domain (RD, residues 1-119) and a C-terminal DNA-binding domain (DBD, residues 130-236). Phosphorylation of kpRstA induces dimerization, which allows two kpRstA DBDs to bind to a tandem repeat, called the RstA box, and regulate the expression of downstream genes. Here we report the solution and crystal structures of the free kpRstA RD, DBD and DBD/RstA box DNA complex. The structure of the kpRstA DBD/RstA box complex suggests that the two protomers interact with the RstA box in an asymmetric fashion. Equilibrium binding studies further reveal that the two protomers within the kpRstA dimer bind to the RstA box in a sequential manner. Taken together, our results suggest a binding model where dimerization of the kpRstA RDs provides the platform to allow the first kpRstA DBD protomer to anchor protein-DNA interaction, whereas the second protomer plays a key role in ensuring correct recognition of the RstA box.


    Organizational Affiliation

    Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC Genomics Research Center, Academia Sinica, Taipei 115, Taiwan, ROC Department of Physics, National Taiwan Normal University, Taipei 116, Taiwan, ROC bmthh@ibms.sinica.edu.tw.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-binding transcriptional regulator RstAAB119Klebsiella pneumoniaeMutation(s): 2 
Gene Names: rstAKPN2242_10390KPR_2822
Find proteins for A6T8N1 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6T8N1 
Go to UniProtKB:  A6T8N1
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*GP*GP*TP*TP*GP*TP*AP*CP*AP*TP*TP*CP*CP*GP*TP*TP*AP*CP*TP*CP*CP*CP*T)-3'C23N/A
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(*CP*AP*GP*GP*GP*AP*GP*TP*AP*AP*CP*GP*GP*AP*AP*TP*GP*TP*AP*CP*AP*AP*C)-3'D23N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.935α = 90
b = 33.313β = 90
c = 72.779γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2013-11-05 
  • Released Date: 2014-07-16 
  • Deposition Author(s): Li, Y.C., Hsiao, C.D.

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2014-08-13
    Changes: Database references