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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1126/science.1163806
  • Primary Citation of Related Structures:  3DNT, 3DNU, 3DNV, 3DNW, 3FBR

  • 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 no ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein hipA
A
440Escherichia coli (strain K12)Gene Names: hipA
EC: 2.7.11.1
Find proteins for P23874 (Escherichia coli (strain K12))
Go to UniProtKB:  P23874
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HTH-type transcriptional regulator hipB
B
88Escherichia coli (strain K12)Gene Names: hipB
Find proteins for P23873 (Escherichia coli (strain K12))
Go to UniProtKB:  P23873
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*DAP*DCP*DTP*DAP*DTP*DCP*DCP*DCP*DCP*DTP*DTP*DAP*DAP*DGP*DGP*DGP*DGP*DAP*DTP*DAP*DG)-3'T21N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ATPKd: 15000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.265 
  • Space Group: P 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 167.250α = 90.00
b = 167.250β = 90.00
c = 62.370γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
CNSrefinement
SCALAdata scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-06-23 
  • Released Date: 2009-07-28 
  • Deposition Author(s): Schumacher, M.A.
  • This entry supersedes: 3DNW

Revision History 

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance