SASDBG7: Dps1, DNA binding protein under starvation conditions (SEC-SAXS)

Basic information

• Entry: Database: SASBDB / ID: SASDBG7

Sample

Dps1, DNA binding protein under starvation conditions (SEC-SAXS)

• DNA protection during starvation protein 1 (protein), Dps1, Deinococcus radiodurans R1

Function / homology

Function:

Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / ferric iron binding / intracellular iron ion homeostasis / DNA binding / cytoplasm

Domain/homology:

Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily

Component:

DNA protection during starvation protein 1

• Biological species: Deinococcus radiodurans R1 (radioresistant)
• Citation: Journal: J Mol Biol / Year: 2017; Title: SAXS Structural Studies of Dps from Deinococcus radiodurans Highlights the Conformation of the Mobile N-Terminal Extensions.; Authors: Sandra P Santos / Maxime G Cuypers / Adam Round / Stephanie Finet / Theyencheri Narayanan / Edward P Mitchell / Célia V Romão / ; Abstract: The radiation-resistant bacterium Deinococcus radiodurans contains two DNA-binding proteins from starved cells (Dps): Dps1 (DR2263) and Dps2 (DRB0092). These are suggested to play a role in DNA interaction and manganese and iron storage. The proteins assemble as a conserved dodecameric structure with structurally uncharacterised N-terminal extensions. In the case of DrDps1, these extensions have been proposed to be involved in DNA interactions, while in DrDps2, their function has yet to be established. The reported data reveal the relative position of the N-terminal extensions to the dodecameric sphere in solution for both Dps. The low-resolution small angle X-ray scattering (SAXS) results show that the N-terminal extensions protrude from the spherical shell of both proteins. The SAXS envelope of a truncated form of DrDps1 without the N-terminal extensions appears as a dodecameric sphere, contrasting strongly with the protrusions observed in the full-length models. The effect of iron incorporation into DrDps2 was investigated by static and stopped-flow SAXS measurements, revealing dynamic structural changes upon iron binding and core formation, as reflected by a quick alteration of its radius of gyration. The truncated and full-length versions of DrDps were also compared on the basis of their interaction with DNA to analyse functional roles of the N-terminal extensions. DrDps1 N-terminal protrusions appear to be directly involved with DNA, whilst those from DrDps2 are indirectly associated with DNA binding. Furthermore, detection of DrDps2 in the D. radiodurans membrane fraction suggests that the N-terminus of the protein interacts with the membrane.

Contact author

• Sandra Santos (Instituto de Tecnologia Química e Biológica António Xavier, Universidade de Lisboa, Oeiras, Portugal)

Models

• Model #887: ; Type: dummy / Software: (2.2i) / Radius of dummy atoms: 1.90 A / Symmetry: P23 / Chi-square value: 11.0224 / P-value: 0.000090; Search similar-shape structures of this assembly by Omokage search (details)
• Model #888: ; Type: dummy / Software: (2.1) / Radius of dummy atoms: 1.90 A / Symmetry: P23 / Chi-square value: 11.935 / P-value: 0.000100; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Dps1, DNA binding protein under starvation conditions (SEC-SAXS); Specimen concentration: 10 mg/ml
• Buffer: Name: 20 mM Tris-HCl, 150 mM NaCl / pH: 7.5

Entity #424

Name: Dps1 / Type: protein / Description: DNA protection during starvation protein 1 / Formula weight: 23.02 / Num. of mol.: 12 / Source: Deinococcus radiodurans R1 / References: UniProt: Q9RS64
Sequence:

MTKKSTKSEA ASKTKKSGVP ETGAQGVRAG GADHADAAHL GTVNNALVNH HYLEEKEFQT VAETLQRNLA TTISLYLKFK KYHWDIRGRF FRDLHLAYDE FIAEIFPSID EQAERLVALG GSPLAAPADL ARYSTVQVPQ ETVRDARTQV ADLVQDLSRV GKGYRDDSQA CDEANDPVTA DMYNGYAATI DKIRWMLQAI MDDERLD

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.09919 Å / Dist. spec. to detc.: 2.80999 mm
• Detector: Name: Pilatus 1M

Scan

Title: Dps1, DNA binding protein under starvation conditi / Measurement date: Nov 22, 2013 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 1500 / Unit: 1/nm /

	Min	Max
Q	0.1056	4.485

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 429 /

	Min	Max
Q	0.16164	2.00649
P(R) point	1	429
R	0	12.75

Result

Type of curve: sec /

	Experimental	Porod
MW	256.97 kDa	256.97 kDa
Volume	-	436.85 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	50.75	0.04	50.76	0.12
Radius of gyration, Rg	4.14 nm	0.004	4.17 nm	0.16

	Min	Max
D	-	12.75
Guinier point	17	49