9CHN | pdb_00009chn

P. vulgaris trimeric HigBA- operator 2 DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Antitoxin control of optimal transcriptional repression in the atypical HigB-HigA toxin-antitoxin system from Proteus vulgaris.

Pavelich, I.J.Schureck, M.A.Srinivas, P.Blackburn, T.M.Wang, D.Hoffer, E.D.Boamah, M.Zaldana, K.Onuoha, N.Miles, S.J.Grabowicz, M.Okafor, C.D.Dunham, C.M.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf610
  • Primary Citation of Related Structures:  
    9CHL, 9CHN

  • PubMed Abstract: 

    Bacterial toxin-antitoxin (TA) pairs transcriptionally autoregulate their expression via a repression/derepression mechanism in response to changing environmental conditions. The structural diversity of TA systems influences the mechanisms of transcriptional regulation. Here, we define the molecular mechanism for the plasmid-encoded HigB-HigA TA pair originally identified in a post-operative infection with antibiotic-resistant Proteus vulgaris. We determine DNA binding and promoter activity by the HigB-HigA complex supported by structural biology and molecular dynamics simulations of an elusive DNA operator-TA repressor complex. To define the optimal oligomeric TA repressor-DNA operator complex required for derepression, we engineered a dedicated trimeric HigB-HigA2 complex that represses transcription more than 26-fold as compared to the tetrameric HigB2-HigA2. These results expand the known diversity of how the HigB-HigA TA family is autoregulated.


  • Organizational Affiliation
    • Department of Chemistry and the Emory Antibiotic Resistance Center, Emory University, Atlanta, GA 30322, United States.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antitoxin HigA
A, C
104Proteus vulgarisMutation(s): 0 
Gene Names: higA
UniProt
Find proteins for Q7A224 (Proteus vulgaris)
Explore Q7A224 
Go to UniProtKB:  Q7A224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7A224
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Endoribonuclease HigB93Proteus vulgarisMutation(s): 0 
Gene Names: higB
EC: 3.1
UniProt
Find proteins for Q7A225 (Proteus vulgaris)
Explore Q7A225 
Go to UniProtKB:  Q7A225
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7A225
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*CP*AP*CP*CP*AP*TP*GP*TP*AP*AP*TP*AP*C)-3')21Proteus vulgaris
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*AP*TP*TP*AP*CP*AP*TP*GP*GP*TP*GP*TP*GP*TP*AP*AP*TP*AP*C)-3')21Proteus vulgaris
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth B]
I [auth D]
J [auth D]
F [auth A],
G [auth A],
H [auth B],
I [auth D],
J [auth D],
K [auth E],
L [auth E],
M [auth E],
N [auth E],
O [auth E],
P [auth E],
Q [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.218 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.82α = 90
b = 139.82β = 90
c = 80.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--
Other governmentUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references