SASDD55: Type II toxin-antitoxin system HicB family antitoxin - HicB prote...

Basic information

• Entry: Database: SASBDB / ID: SASDD55

Sample

Type II toxin-antitoxin system HicB family antitoxin - HicB protein - bound to addiction module toxin, HicAToxin-antitoxin system

• Type II toxin-antitoxin system HicB family antitoxinToxin-antitoxin system (protein), HicB, Burkholderia pseudomallei
• Addiction module toxin, HicA (protein), HicA2-Hydroxyisocaproic acid, Burkholderia pseudomallei

Function / homology

Function:

hydrolase activity / mRNA binding

Domain/homology:

HicA mRNA interferase family / HicA superfamily / HicA toxin of bacterial toxin-antitoxin, / HicB-like antitoxin of toxin-antitoxin system / HicB_like antitoxin of bacterial toxin-antitoxin system / TTHA1013/TTHA0281-like

Component:

HicB-like antitoxin of toxin-antitoxin system domain-containing protein / Addiction module toxin, HicA family

• Biological species: Burkholderia pseudomallei (bacteria)
• Citation: Journal: J Biol Chem / Year: 2018; Title: The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.; Authors: Ashley J Winter / Christopher Williams / Michail N Isupov / Hannah Crocker / Mariya Gromova / Philip Marsh / Oliver J Wilkinson / Mark S Dillingham / Nicholas J Harmer / Richard W Titball / Matthew P Crump / ; Abstract: Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which both toxins and antitoxins are proteins. The HicAB system is one of the prototypic TA systems, found in many bacterial species. Complex interactions between the protein toxin (HicA), the protein antitoxin (HicB), and the DNA upstream of the encoding genes regulate the activity of this system, but few structural details are available about how HicA destabilizes the HicB-DNA complex. Here, we determined the X-ray structures of HicB and the HicAB complex to 1.8 and 2.5 Å resolution, respectively, and characterized their DNA interactions. This revealed that HicB forms a tetramer and HicA and HicB form a heterooctameric complex that involves structural reorganization of the C-terminal (DNA-binding) region of HicB. Our observations indicated that HicA has a profound impact on binding of HicB to DNA sequences upstream of in a stoichiometric-dependent way. At low ratios of HicA:HicB, there was no effect on DNA binding, but at higher ratios, the affinity for DNA declined cooperatively, driving dissociation of the HicA:HicB:DNA complex. These results reveal the structural mechanisms by which HicA de-represses the HicB-DNA complex.

Contact author

• Ash Winter (University of Bristol)

Models

• Model #1881: ; Type: atomic / Chi-square value: 2.87828639506; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Type II toxin-antitoxin system HicB family antitoxin - HicB protein - bound to addiction module toxin, HicAToxin-antitoxin system; Specimen concentration: 5 mg/ml / Entity id: 1010 / 1011
• Buffer: Name: 25 mM Tris 150 mM NaCl / pH: 7.5

Entity #1010

Name: HicB / Type: protein
Description: Type II toxin-antitoxin system HicB family antitoxinToxin-antitoxin system
Formula weight: 15.739 / Num. of mol.: 4 / Source: Burkholderia pseudomallei / References: UniProt: Q63NA5
Sequence:

MMEFPIAVHK DDGSVYGVTV PDIPGVHSWG ETIDDAIKNT REAIVGHVET LIELGEDVEF TCSTVEELVA KPEYAGAVWA LVSVDLSQLD SKPERINVSI PRFVLHKIDA YVASRHETRS GFLARAALEA LNEGKKHHHH HH

Entity #1011

Name: HicA2-Hydroxyisocaproic acid / Type: protein / Description: Addiction module toxin, HicA / Formula weight: 7.052 / Num. of mol.: 1 / Source: Burkholderia pseudomallei / References: UniProt: Q63NA6
Sequence:

GIDPFTNSSK LIRMLEEDGW RLVRVTGSAH HFKHPKKPGL VTVPHPKKDL PIGTVKSIQK SAGL

Experimental information

• Beam: Instrument name: Diamond Light Source B21 / City: Oxfordshire / 国: UK / Shape: 1 x 5 mm / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 4.014 mm
• Detector: Name: Pilatus 2M

Scan

Title: Type II toxin-antitoxin system HicB family antitoxin, HicB, bound to addiction module toxin, HicA
Measurement date: Jul 27, 2016 / Storage temperature: 4 °C / Cell temperature: 25 °C / Exposure time: 3 sec. / Unit: 1/A /

	Min	Max
Q	0.004	0.4075

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 1036 /

	Min	Max
Q	0.00786318	0.292355
P(R) point	1	1036
R	0	110

Result

Type of curve: sec
Comments: Analysis of the data involved ScÅtter (www.bioisis.net/). The resultant curve was fit with the crystal structure of HicB, PDB Code: 6G26.

	Experimental	Porod
MW	74 kDa	67 kDa
Volume	-	110 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.003642	1.0E-5	0.003635	9.6E-6
Radius of gyration, Rg	3.224 nm	0.09	3.197 nm	0.052

	Min	Max
D	-	11
Guinier point	15	135