3HZI

Structure of mdt protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB.

Schumacher, M.A.Piro, K.M.Xu, W.Hansen, S.Lewis, K.Brennan, R.G.

(2009) Science 323: 396-401

  • DOI: https://doi.org/10.1126/science.1163806
  • Primary Citation of Related Structures:  
    3DNT, 3DNU, 3DNV, 3FBR, 3HZI

  • PubMed Abstract: 

    Bacterial multidrug tolerance is largely responsible for the inability of antibiotics to eradicate infections and is caused by a small population of dormant bacteria called persisters. HipA is a critical Escherichia coli persistence factor that is normally neutralized by HipB, a transcription repressor, which also regulates hipBA expression. Here, we report multiple structures of HipA and a HipA-HipB-DNA complex. HipA has a eukaryotic serine/threonine kinase-like fold and can phosphorylate the translation factor EF-Tu, suggesting a persistence mechanism via cell stasis. The HipA-HipB-DNA structure reveals the HipB-operator binding mechanism, approximately 70 degrees DNA bending, and unexpected HipA-DNA contacts. Dimeric HipB interacts with two HipA molecules to inhibit its kinase activity through sequestration and conformational inactivation. Combined, these studies suggest mechanisms for HipA-mediated persistence and its neutralization by HipB.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Texas, M. D. Anderson Cancer Center, Unit 1000, Houston, TX 77030, USA. maschuma@mdanderson.org


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein hipA440Escherichia coli K-12Mutation(s): 1 
Gene Names: hipAb1507JW1500
EC: 2.7.11.1
UniProt
Find proteins for P23874 (Escherichia coli (strain K12))
Explore P23874 
Go to UniProtKB:  P23874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23874
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HTH-type transcriptional regulator hipB88Escherichia coli K-12Mutation(s): 0 
Gene Names: hipBb1508JW1501
UniProt
Find proteins for P23873 (Escherichia coli (strain K12))
Explore P23873 
Go to UniProtKB:  P23873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23873
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*DGP*DGP*DGP*DGP*DAP*DTP*DAP*DG)-3'C [auth T]21N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
ATP PDBBind:  3HZI Kd: 1.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.25α = 90
b = 167.25β = 90
c = 62.37γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-01-15
    Changes: Derived calculations
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-22
    Changes: Data collection
  • Version 1.6: 2024-10-30
    Changes: Structure summary