SASDDH3: Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2)

Basic information

• Entry: Database: SASBDB / ID: SASDDH3

Sample

Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2)

• Transcriptional regulator Lrs14-like protein (protein), AbfR2, Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)

• Function / homology: Transcription regulator TrmB, N-terminal / Sugar-specific transcriptional regulator TrmB / helix_turn_helix, Arsenical Resistance Operon Repressor / HTH ArsR-type DNA-binding domain / ArsR-like helix-turn-helix domain / Winged helix DNA-binding domain superfamily / DNA-binding transcription factor activity / Winged helix-like DNA-binding domain superfamily / Transcriptional regulator Lrs14-like protein
• Biological species: Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
• Citation: Journal: Acta Crystallogr D Struct Biol / Year: 2018; Title: Crystal structure of an Lrs14-like archaeal biofilm regulator from Sulfolobus acidocaldarius.; Authors: Marian S Vogt / Simon L Völpel / Sonja Verena Albers / Lars Oliver Essen / Ankan Banerjee / ; Abstract: The small winged helix-turn-helix (wHTH) proteins of the Lrs14 family are major transcriptional regulators and act as archaeal biofilm regulators (AbfRs) in the crenarchaeote Sulfolobus acidocaldarius. Here, the first crystal structure of an AbfR ortholog, AbfR2, the deletion of which is known to impair biofilm formation, is presented. Like most other wHTH orthologs, AbfR2 is dimeric in solution as well as in its 2.45 Å resolution crystal structure. Given the presence of three independent AbfR2 dimers in the asymmetric unit, the crystal structure shows a considerable degree of conformational variation within the dimer, the antiparallel orientations of which are stabilized by coiled-coil interaction between H4 helices. Conserved anchor interactions between helices H0 and H4 of AbfR2 further contribute to dimer stabilization. The combined structural and bioinformatic analysis reveals cluster-specific structural differences between different members of the Lrs14 protein family.

Contact author

• Marian Vogt (University of Marburg, Marburg, Germany)

Models

• Model #1783: ; Type: dummy / Radius of dummy atoms: 2.10 A / Chi-square value: 0.812 / P-value: 0.101902; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1786: ; Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 1.052; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2); Specimen concentration: 0.83 mg/ml
• Buffer: Name: 300 mM NaCl, 20 mM HEPES, pH 7.5 / pH: 7.5

Entity #919

Name: AbfR2 / Type: protein / Description: Transcriptional regulator Lrs14-like protein / Formula weight: 16.368 / Num. of mol.: 2
Source: Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770)
References: UniProt: Q4J9G1
Sequence:

MGSSHHHHHH SQDPNSMETV LQIPYQKKTQ IEKLLEFMYG LNEKEVQLIF RLLYSDTKLN IEELAEEFKV SKALISKSLS ELANKGLIER EKVSNEGRKG RPIYVYYVDR EQLFKRISRD LEELVQASIA KLKEYIFKS

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.124 Å
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Solution Structure of Archaeal Biofilm Regulator 2 (AbfR2)
Measurement date: May 5, 2016 / Storage temperature: 4 °C / Cell temperature: 4 °C / Exposure time: 1 sec. / Number of frames: 10 / Unit: 1/nm /

	Min	Max
Q	0.0348	4.9439

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 449 /

	Min	Max
Q	0.171421	2.28206
P(R) point	1	449
R	0	10

Result

Type of curve: single_conc
Comments: The associated atomic model structure is included for comparative purposes only, i.e., to compare the overall topology of the atomic model with the solution scattering and the DAMMIF bead model. Two fits displayed for the atomic model were calculated using CRYSOL (top) and SASREF (bottom).

	Experimental	Standard	Porod
MW	39 kDa	39.29 kDa	37 kDa
Volume	-	-	56.89 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	24.03	24.16	0.09
Radius of gyration, Rg	2.8 nm	2.85 nm	0.03

	Min	Max
D	-	10
Guinier point	16	72