PDBsum entry 3hzi

Transcription/DNA

PDB id: 3hzi

Contents

Protein chains

423 a.a. *

71 a.a. *

DNA/RNA

Ligands

ATP

SO4 ×9

Waters ×5

* Residue conservation analysis

PDB id:

3hzi

Name:

Transcription/DNA

Title:

Structure of mdt protein

Structure:

Protein hipa. Chain: a. Engineered: yes. Mutation: yes. Hth-type transcriptional regulator hipb. Chain: b. Engineered: yes. 5'-d( Dap Dcp Dtp Dap Dtp Dcp Dcp Dcp Dcp Dtp Dtp Dap Dap D gp Dgp Dgp Dgp Dap Dtp Dap Dg)-3'.

Source:

Escherichia coli. Organism_taxid: 83333. Gene: hipa, b1507, jw1500. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: hipb, b1508, jw1501. Synthetic: yes

Resolution:

2.98Å R-factor: 0.265 R-free: 0.283

Authors:

M.A.Schumacher

Key ref:

M.A.Schumacher et al. (2009). Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB. Science, 323, 396-401. PubMed id: 19150849 DOI: 10.1126/science.1163806

Date:

23-Jun-09 Release date: 28-Jul-09

Supersedes:

3dnw

Protein chain

P23874  (HIPA_ECOLI) -  Serine/threonine-protein kinase toxin HipA from Escherichia coli (strain K12)

Seq: 440 a.a.

Struc: 423 a.a.*

Protein chain

P23873  (HIPB_ECOLI) -  Antitoxin HipB from Escherichia coli (strain K12)

Seq: 88 a.a.

Struc: 71 a.a.

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chain

A-C-T-A-T-C-C-C-C-T-T-A-A-G-G-G-G-A-T-A-G 21 bases

Enzyme reactions

• Enzyme class: Chain A: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

L-seryl-[protein] (Bound ligand (Het Group name = ATP) corresponds exactly) + ATP = O-phospho-L-seryl-[protein] + ADP + H(+)

L-threonyl-[protein] (Bound ligand (Het Group name = ATP) corresponds exactly) + ATP = O-phospho-L-threonyl-[protein] + ADP + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1126/science.1163806

Science 323:396-401 (2009)

PubMed id: 19150849

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

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

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.

Selected figure(s)

Figure 2.
Fig. 2. Crystal structure of the HipA-HipB-DNA complex. (A) Ribbon diagram of the HipA-HipB-DNA operator complex. The two HipA monomers are blue, and one subunit of the HipB dimer is yellow and the other orange. The N and C termini and secondary structural elements of one HipB subunit (orange) are labeled. β1' is labeled for the yellow subunit. Also labeled are the N and C domains of each HipA molecule. The DNA is shown as sticks with carbon, nitrogen, oxygen, and phosphorus atoms colored green, blue, red, and magenta, respectively. (B) Superimposition of substrate-free HipA (red) onto HipB-bound HipA (blue), showing their essentially identical conformations. For clarity, only one HipA molecule in the HipA-HipB-DNA complex is shown. (C) Closeup of the HipA-HipB interaction interface. Each lateral side of the HipB dimer, labeled subunits 1 and 2, interacts with the N and C domains of one HipA monomer. The DNA is shown as a gray surface. For clarity, only one HipA molecule is shown because the interaction interface between the other HipA molecule and the HipB dimer is identical. The residues that contribute to the interface are labeled and shown as orange sticks for HipB and dark blue sticks for HipA.

Figure 3.
Fig. 3. HipB and HipA interactions with the hipB operator DNA. (A) Schematic representation of HipB-HipA-DNA interactions. Only one half site of the 21-oligomer duplex is shown because the identical contacts are made with each half site. The strands are labeled 1A to 10A and 1B to 10B. Bases are represented as rectangles and labeled according to sequence. The ribose groups are shown as pentagons. The operator signature motif sequence, TATCC, is red. HipB-DNA contacts are yellow. Hydrophobic contacts are indicated by lines and hydrogen bonds are indicated by arrows. Blue arrows indicate HipA-phosphate contacts. (B) HipB-DNA interactions. Only one HipB subunit-DNA half site is shown. The DNA and residues making side-chain contacts are shown as sticks. The signature motif sequence, TATCC, is labeled in red. For clarity, only the four-helix bundle is shown and labeled. (C) HipA-DNA contacts. The HipB dimer (yellow) is shown for reference. The location of the two DNA-interacting residues from HipA, K379 and R382, are shown as blue sticks and highlighted by mesh surface representations. The DNA is shown as sticks and colored as in (B). (D) HipA-HipB bound DNA is bent. This is an omit F[o]-F[c] map in which the DNA was omitted from refinement to 2.68 Å resolution. The map is contoured at 2.8 . The DNA is shown as sticks and the bend angle is indicated.

The above figures are reprinted from an Open Access publication published by the AAAs: Science (2009, 323, 396-401) copyright 2009.

Figures were selected by an automated process.