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

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Basic information

Entry
Database: SASBDB / ID: SASDD55
SampleType II toxin-antitoxin system HicB family antitoxin - HicB protein - bound to addiction module toxin, HicA
  • Type II toxin-antitoxin system HicB family antitoxin (protein), HicB, Burkholderia pseudomallei
  • Addiction module toxin, HicA (protein), HicA, Burkholderia pseudomallei
Function / homology
Function and homology information


hydrolase activity / mRNA binding
Similarity search - Function
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
Similarity search - Domain/homology
HicB-like antitoxin of toxin-antitoxin system domain-containing protein / Addiction module toxin, HicA family
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
CitationJournal: 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 ...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)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Models

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

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Sample

SampleName: Type II toxin-antitoxin system HicB family antitoxin - HicB protein - bound to addiction module toxin, HicA
Specimen concentration: 5 mg/ml / Entity id: 1010 / 1011
BufferName: 25 mM Tris 150 mM NaCl / pH: 7.5
Entity #1010Name: HicB / Type: protein
Description: Type II toxin-antitoxin system HicB family antitoxin
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 #1011Name: HicA / 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

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Experimental information

BeamInstrument name: Diamond Light Source B21 / City: Oxfordshire / 国: UK / Shape: 1 x 5 mm / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 4.014 mm
DetectorName: 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 /
MinMax
Q0.004 0.4075
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 1036 /
MinMax
Q0.00786318 0.292355
P(R) point1 1036
R0 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.
ExperimentalPorod
MW74 kDa67 kDa
Volume-110 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.003642 1.0E-5 0.003635 9.6E-6
Radius of gyration, Rg3.224 nm0.09 3.197 nm0.052

MinMax
D-11
Guinier point15 135

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