SASDG25: DNA repair protein Rad5 (with 6xhis and twin-strep tags)

Basic information

• Entry: Database: SASBDB / ID: SASDG25

Sample

DNA repair protein Rad5 (with 6xhis and twin-strep tags)

• DNA repair protein RAD5 (protein), Rad5, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Function / homology

Function:

error-free postreplication DNA repair / free ubiquitin chain polymerization / Y-form DNA binding / four-way junction helicase activity / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / postreplication repair / ATP-dependent chromatin remodeler activity / error-free translesion synthesis / ATP-dependent activity, acting on DNA / error-prone translesion synthesis / four-way junction DNA binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein polyubiquitination / double-strand break repair / chromosome, telomeric region / DNA repair / chromatin / zinc ion binding / ATP binding / nucleus / cytoplasm

Domain/homology:

HIRAN domain / HIRAN domain / HIRAN / Ring finger domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Helicase conserved C-terminal domain / Zinc finger RING-type profile. / Zinc finger, RING-type / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase

Component:

DNA repair protein RAD5

• Biological species: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

Contact author

• Melissa Gildenberg (University of Iowa Carver College of Medicine, Iowa, USA)

Models

• Model #3701: ; Type: dummy / P-value: 0.409692
• Model #3702: ; Type: dummy

Sample

• Sample: Name: DNA repair protein Rad5 (with 6xhis and twin-strep tags); Specimen concentration: 7.75 mg/ml
• Buffer: Name: 40 mM Tris, 150 mM KCl, 5 mM DTT, 5% glycerol / pH: 8

Entity #1818

Name: Rad5 / Type: protein / Description: DNA repair protein RAD5 / Formula weight: 137.693 / Num. of mol.: 1
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P32849
Sequence:

MHHHHHHSHI EQEERKRFFN DDLDTSETSL NFKSENKESF LFANSHNDDD DDVVVSVSDT TEGEGDRSIV PVRREIEEEG QNQFITELLR IIPEMPKDLV MELNEKFGSQ EEGLSLALSH YFDHNSGTSI SKIPSSPNQL NTLSDTSNST LSPSSFHPKR RRIYGFRNQT RLEDKVTWKR FIGALQVTGM ATRPTVRPLK YGSQMKLKRS SEEISATKVY DSRGRKKASM ASLVRIFDIQ YDREIGRVSE DIAQILYPLL SSHEISFEVT LIFCDNKRLS IGDSFILQLD CFLTSLIFEE RNDGESLMKR RRTEGGNKRE KDNGNFGRTL TETDEELESR SKRLALLKLF DKLRLKPILD EQKALEKHKI ELNSDPEIID LDNDEICSNQ VTEVHNNLRD TQHEEETMNL NQLKTFYKAA QSSESLKSLP ETEPSRDVFK LELRNYQKQG LTWMLRREQE FAKAASDGEA SETGANMINP LWKQFKWPND MSWAAQNLQQ DHVNVEDGIF FYANLHSGEF SLAKPILKTM IKGGILSDEM GLGKTVAAYS LVLSCPHDSD VVDKKLFDIE NTAVSDNLPS TWQDNKKPYA SKTTLIVVPM SLLTQWSNEF TKANNSPDMY HEVYYGGNVS SLKTLLTKTK TPPTVVLTTY GIVQNEWTKH SKGRMTDEDV NISSGLFSVN FYRIIIDEGH NIRNRTTVTS KAVMALQGKC KWVLTGTPII NRLDDLYSLV KFLELDPWRQ INYWKTFVST PFESKNYKQA FDVVNAILEP VLLRRTKQMK DKDGKPLVEL PPKEVVIKRL PFSKSQDLLY KFLLDKAEVS VKSGIARGDL LKKYSTILVH ILRLRQVCCH PGLIGSQDEN DEDLSKNNKL VTEQTVELDS LMRVVSERFD NSFSKEELDA MIQRLKVKYP DNKSFQSLEC SICTTEPMDL DKALFTECGH SFCEKCLFEY IEFQNSKNLG LKCPNCRNQI DACRLLALVQ TNSNSKNLEF KPYSPASKSS KITALLKELQ LLQDSSAGEQ VVIFSQFSTY LDILEKELTH TFSKDVAKIY KFDGRLSLKE RTSVLADFAV KDYSRQKILL LSLKAGGVGL NLTCASHAYM MDPWWSPSME DQAIDRLHRI GQTNSVKVMR FIIQDSIEEK MLRIQEKKRT IGEAMDTDED ERRKRRIEEI QMLFEWSHPQ FEKGGGSGGG SGGSAWSHPQ FEK

Experimental information

• Beam: Instrument name: Advanced Photon Source (APS), Argonne National Laboratory BioCAT 18ID; City: Lemont, IL / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1033 Å / Dist. spec. to detc.: 3.5 mm
• Detector: Name: Pilatus3 X 1M / Pixsize x: 0.172 mm

Scan

Title: DNA repair protein Rad5 (with 6xhis and twin-strep tags)
Measurement date: Mar 6, 2019 / Storage temperature: 4 °C / Cell temperature: 20 °C / Exposure time: 0.5 sec. / Number of frames: 19 / Unit: 1/A /

	Min	Max
Q	0.0046	0.3627

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 1243 /

	Min	Max
Q	0.00575145	0.362433
P(R) point	1	1243
R	0	178

Result

Type of curve: sec
Comments: The simulation code uiowa_BD was used to carry out Langevin dynamics (LD) simulations of Rad5. Two different sets of simulations were carried out in triplicate, with each set using a different starting model of Rad5. The different starting models were generated based on docking results from two different docking servers, ClusPro and ZDOCK. Docking was used to position the HIRAN domain on the helicase domain in an acceptable orientation. For each simulation, a time-step of 125 fs was used, and a snapshot (PDB file) was recorded every ns of simulation time for a total of 5 µs of simulation time. As such, each simulation generated a total of 5000 individual structures. The first set of models displayed in this entry (top) are representatives from the ZDOCK LD simulation while the second set of models (bottom) are representatives derived from ClusPro. A zip file containing the three replicates of each ClusPro and ZDOCK simulation are attached to this entry and made available in the full entry zip archive (5000 PDB files per simulation; ca. 2.2 GB total).

	Experimental	Porod
MW	140 kDa	-
Volume	-	254 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	6.103E-5	2.32E-7	6.043E-5	2.302E-7
Radius of gyration, Rg	4.92 nm	0.031	4.7 nm	0.03

	Min	Max
D	-	17.8
Guinier point	7	81