2WIU | pdb_00002wiu

Mercury-modified bacterial persistence regulator hipBA

• PDB DOI: https://doi.org/10.2210/pdb2WIU/pdb

• Classification: TRANSFERASE/TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-05-17 Released: 2009-07-28 
• Deposition Author(s): Evdokimov, A., Voznesensky, I., Fennell, K., Anderson, M., Smith, J.F., Fisher, D.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.264 (Depositor) 
• R-Value Work: 
  0.216 (Depositor) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

New Kinase Regulation Mechanism Found in Hipba: A Bacterial Persistence Switch.

Evdokimov, A., Voznesensky, I., Fennell, K., Anderson, M., Smith, J.F., Fisher, D.A.

(2009) Acta Crystallogr D Biol Crystallogr 65: 875

• PubMed: 19622872 
• DOI: https://doi.org/10.1107/S0907444909018800
• Primary Citation Related Structures: 
  2WIU


• PubMed Abstract: 
  

  Bacterial persistence is the ability of individual cells to randomly enter a period of dormancy during which the cells are protected against antibiotics. In Escherichia coli, persistence is regulated by the activity of a protein kinase HipA and its DNA-binding partner HipB, which is a strong inhibitor of both HipA activity and hip operon transcription. The crystal structure of the HipBA complex was solved by application of the SAD technique to a mercury derivative. In this article, the fortuitous and interesting effect of mercury soaks on the native HipBA crystals is discussed as well as the intriguing tryptophan-binding pocket found on the HipA surface. A HipA-regulation model is also proposed that is consistent with the available structural and biochemical data.

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Organizational Affiliation: 
• Pfizer Inc, Groton, Connecticut, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 122.14 kDa 
• Atom Count: 8,029 
• Modeled Residue Count: 974 
• Deposited Residue Count: 1,068 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN HIPA	A, C	446	Escherichia coli	Mutation(s): 0  EC: 2.7.11.1
UniProt
Find proteins for P23874 (Escherichia coli (strain K12)) Explore P23874  Go to UniProtKB:  P23874

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HTH-TYPE TRANSCRIPTIONAL REGULATOR HIPB	B, D	88	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P23873 (Escherichia coli (strain K12)) Explore P23873  Go to UniProtKB:  P23873

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HG	E [auth A], F [auth A], J [auth B], M [auth C], N [auth C], O [auth C], S [auth D]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], P [auth C], Q [auth C], R [auth C], T [auth D], U [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.264 (Depositor) 
• R-Value Work:  0.216 (Depositor) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.933	α = 90
b = 166.933	β = 90
c = 124.577	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-28 
Deposition Author(s): Evdokimov, A., Voznesensky, I., Fennell, K., Anderson, M., Smith, J.F., Fisher, D.A.

Revision History  

• Version 1.0: 2009-07-28
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other