2M87 | pdb_00002m87

Structural Basis of DNA Recognition by the Effector Domain of Klebsiella pneumoniae PmrA

• PDB DOI: https://doi.org/10.2210/pdb2M87/pdb
• BMRB: 19231

• Classification: SIGNALING PROTEIN
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae ST512-K30BO
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-07 Released: 2014-01-22 
• Deposition Author(s): Wang, I., Lou, Y.C., Chen, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure and tandem DNA recognition of the C-terminal effector domain of PmrA from Klebsiella pneumoniae.

Lou, Y.C., Wang, I., Rajasekaran, M., Kao, Y.F., Ho, M.R., Hsu, S.T., Chou, S.H., Wu, S.H., Chen, C.

(2014) Nucleic Acids Res 42: 4080-4093

• PubMed: 24371275 
• DOI: https://doi.org/10.1093/nar/gkt1345
• Primary Citation Related Structures: 
  2M87


• PubMed Abstract: 
  

  Klebsiella pneumoniae PmrA is a polymyxin-resistance-associated response regulator. The C-terminal effector/DNA-binding domain of PmrA (PmrAC) recognizes tandem imperfect repeat sequences on the promoters of genes to induce antimicrobial peptide resistance after phosphorylation and dimerization of its N-terminal receiver domain (PmrAN). However, structural information concerning how phosphorylation of the response regulator enhances DNA recognition remains elusive. To gain insights, we determined the nuclear magnetic resonance solution structure of PmrAC and characterized the interactions between PmrAC or BeF3(-)-activated full-length PmrA (PmrAF) and two DNA sequences from the pbgP promoter of K. pneumoniae. We showed that PmrAC binds to the PmrA box, which was verified to contain two half-sites, 5'-CTTAAT-3' and 5'-CCTAAG-3', in a head-to-tail fashion with much stronger affinity to the first than the second site without cooperativity. The structural basis for the PmrAC-DNA complex was investigated using HADDOCK docking and confirmed by paramagnetic relaxation enhancement. Unlike PmrAC, PmrAF recognizes the two sites simultaneously and specifically. In the PmrAF-DNA complex, PmrAN may maintain an activated homodimeric conformation analogous to that in the free form and the interactions between two PmrAC molecules aid in bending and binding of the DNA duplex for transcription activation.

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Organizational Affiliation: 
• Institute of Biomedical Sciences, Institute of Biological Chemistry, Academia Sinica, Taipei 115, Institute of Biochemistry and Agricultural Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan, Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.85 kDa 
• Atom Count: 833 
• Modeled Residue Count: 103 
• Deposited Residue Count: 103 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulatory protein basR/pmrA	A	103	Klebsiella pneumoniae subsp. pneumoniae ST512-K30BO	Mutation(s): 0  Gene Names: BN18_3635

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-22 
Deposition Author(s): Wang, I., Lou, Y.C., Chen, C.

Revision History  

• Version 1.0: 2014-01-22
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Data collection, Database references
• Version 1.2: 2023-06-14
  Changes: Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references