Regulatory domain of HypT M206Q mutant from Salmonella typhimurium

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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This is version 1.2 of the entry. See complete history


Structural basis for HOCl recognition and regulation mechanisms of HypT, a hypochlorite-specific transcriptional regulator.

Jo, I.Kim, D.No, T.Hong, S.Ahn, J.Ryu, S.Ha, N.C.

(2019) Proc Natl Acad Sci U S A 116: 3740-3745

  • DOI: https://doi.org/10.1073/pnas.1811509116
  • Primary Citation of Related Structures:  
    5YDO, 5YDV, 5YDW, 5YER, 5YEZ

  • PubMed Abstract: 

    Hypochlorous acid (HOCl) is generated in the immune system to kill microorganisms. In Escherichia coli , a hypochlorite-specific transcription regulator, HypT, has been characterized. HypT belongs to the LysR-type transcriptional regulator (LTTR) family that contains a DNA-binding domain (DBD) and a regulatory domain (RD). Here, we identified a hypT gene from Salmonella enterica serovar Typhimurium and determined crystal structures of the full-length HypT protein and the RD. The full-length structure reveals a type of tetrameric assembly in the LTTR family. Based on HOCl-bound and oxidation-mimicking structures, we identified a HOCl-driven methionine oxidation mechanism, in which the bound HOCl oxidizes a conserved methionine residue lining the putative ligand-binding site in the RD. Furthermore, we proposed a molecular model for the oxidized HypT, where methionine oxidation by HOCl results in a conformational change of the RD, inducing a counter rotation of the DBD dimers. Target genes that are regulated by HypT and their roles in Salmonella were also investigated. DNase I footprinting experiments revealed a DNA segment containing two pseudopalindromic motifs that are separated by ∼100 bp, suggesting that only the oxidized structure makes a concomitant binding, forming a DNA loop. An understanding of the HypT-mediated mechanism would be helpful for controlling many pathogenic bacteria by counteracting bacterial HOCl defense mechanisms.

  • Organizational Affiliation

    Department of Agricultural Biotechnology, Seoul National University, 08826 Seoul, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell density-dependent motility repressor
A, B, C, D
209Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 1 
Gene Names: qseD_2DD95_15310STMU2UK_04484
Find proteins for Q7CP75 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q7CP75 
Go to UniProtKB:  Q7CP75
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7CP75
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.204α = 90
b = 67.326β = 90
c = 192.255γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description