SASDCB3: Methylated C-terminal ZBTB38 binding sequence (mCZ38BS)

Basic information

• Entry: Database: SASBDB / ID: SASDCB3

Sample

Methylated C-terminal ZBTB38 binding sequence (mCZ38BS)

• methylated C-terminal ZBTB38 binding sequence (DNA), mCZ38BS

• Citation: Journal: J Mol Biol / Year: 2018; Title: The C-Terminal Zinc Fingers of ZBTB38 are Novel Selective Readers of DNA Methylation.; Authors: Amir Pozner / Nicholas O Hudson / Jill Trewhella / Tommy W Terooatea / Sven A Miller / Bethany A Buck-Koehntop / ; Abstract: Methyl-CpG binding proteins play an essential role in translating DNA methylation marks into a downstream transcriptional response, which has implications for both normal cell function as well as disease. Although for many of these proteins, a detailed mechanistic understanding for how this cellular process is mediated remains to be determined. ZBTB38 is an under-characterized member of the zinc finger (ZF) family of methyl-CpG binding proteins. Functional knowledge has been gained for its conserved methylated DNA binding N-terminal ZF region; however, a specific role for the C-terminal set of five ZFs remains to be elucidated. Here we demonstrate for the first time that a subset of the C-terminal ZBTB38 ZFs exhibit high-affinity DNA interactions and that preferential targeting of the consensus DNA site is methyl specific. Utilizing a hybrid approach, a model for the C-terminal ZBTB38 ZFs in complex with its cognate DNA target is proposed, providing insight into a possible novel mode of methylated DNA recognition. Furthermore, it is shown that the C-terminal ZFs of ZBTB38 can directly occupy promoters harboring the newly identified sequence motif in cell in a methyl-dependent manner and, depending on the gene context, contribute to modulating transcriptional response. Combined, these findings provide evidence for a key and novel physiological function for the C-terminal ZF domain of ZBTB38.

Contact author

• Jill Trewhella (School of Molecular Bioscience, University of Sydney., Sydney, New South Wales 2006, Australia)

Models

• Model #1236: ; Type: dummy / Radius of dummy atoms: 2.40 A / Comment: methylated C-terminal ZBTB38 binding sequence / Chi-square value: 1.121 / P-value: 0.848600; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Methylated C-terminal ZBTB38 binding sequence (mCZ38BS); Specimen concentration: 4.2 mg/ml
• Buffer: Name: 10 mM Tris, 1 mM tris(2-carboxy-ethyl)phosphine (TCEP), 0.05% NaN3, 10% D2O; pH: 6.8 ; Comment: Solvent blank taken from flow through in concentration step

Entity #666

Name: mCZ38BS / Type: DNA / Description: methylated C-terminal ZBTB38 binding sequence / Formula weight: 16.705 / Num. of mol.: 1
Sequence:

GCACTCATCG GCGCAGATCA GCTAGCCGGC TAGCTGATCT GCGCCGATGA GTGC

Experimental information

• Beam: Instrument name: Department of Chemistry, University of Utah Anton Paar SAXSess; City: Salt Lake City, UT / 国: USA / Type of source: X-ray in house / Wavelength: 0.154 Å / Dist. spec. to detc.: 0.2612 mm
• Detector: Name: Dectris Mythen 1K / Type: 1D diode array detector / Pixsize x: 50 mm

Scan

Title: methylated C-terminal ZBTB38 binding sequence (mCZ38BS)
Measurement date: Oct 27, 2016 / Cell temperature: 22 °C / Exposure time: 30 sec. / Number of frames: 120 / Unit: 1/nm /

	Min	Max
Q	0.1	3.7176

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 475 /

	Min	Max
Q	0.1	3.71761
P(R) point	1	475
R	0	9.2

Result

Type of curve: single_conc

	Experimental	Standard	Porod
MW	16.632 kDa	16.924 kDa	15.3 kDa
Volume	-	-	23 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.1143	0.00149	0.1135	0.0004
Radius of gyration, Rg	2.62 nm	0.06	2.51 nm	0.03

	Min	Max
D	-	9.2
Guinier point	1	52