SASDBU7: DNA binding domain (DBD) of chromo domain-containing protein 1 (C...

Basic information

• Entry: Database: SASBDB / ID: SASDBU7

Sample

DNA binding domain (DBD) of chromo domain-containing protein 1 (Chd1: 1009-1274)

• chromodomain helicase DNA binding domain (protein), Chd1-DBD, Saccharomyces cerevisiae

Function / homology

Function:

nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of DNA-templated DNA replication / regulation of chromatin organization / rDNA binding / nucleosome organization / SLIK (SAGA-like) complex / ATP-dependent chromatin remodeler activity / sister chromatid cohesion / SAGA complex / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / ATP-dependent activity, acting on DNA / methylated histone binding / helicase activity / transcription elongation by RNA polymerase II / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin DNA binding / histone binding / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus

Domain/homology:

Chromodomain helicase DNA-binding domain / Chromodomain helicase DNA-binding domain 1 / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal domain / Chromodomain-helicase-DNA-binding protein 1-like, C-terminal / DUF4208 / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / : / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Helicase conserved C-terminal domain / Homeobox-like domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase

Component:

Chromo domain-containing protein 1

• Biological species: Saccharomyces cerevisiae (brewer's yeast)
• Citation: Journal: Elife / Year: 2017; Title: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes.; Authors: Ramasubramanian Sundaramoorthy / Amanda L Hughes / Vijender Singh / Nicola Wiechens / Daniel P Ryan / Hassane El-Mkami / Maxim Petoukhov / Dmitri I Svergun / Barbara Treutlein / Salina Quack / Monika Fischer / Jens Michaelis / Bettina Böttcher / David G Norman / Tom Owen-Hughes / ; Abstract: The yeast Chd1 protein acts to position nucleosomes across genomes. Here, we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state, the DNA-binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA-binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavorable alignment of C-terminal DNA-binding region in solution contributes to an auto-inhibited state.

Contact author

• Ramasubramanian Sundaramoorthy (University of Dundee, Dundee, UK)

Models

• Model #919: ; Type: dummy / Software: GASBOR (2.3i) / Radius of dummy atoms: 1.90 A / Symmetry: C1 / Chi-square value: 2.10; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: DNA binding domain (DBD) of chromo domain-containing protein 1 (Chd1: 1009-1274); Specimen concentration: 1.20-9.90
• Buffer: Name: 50mM Hepes 150mM NaCl / pH: 7.5

Entity #517

Name: Chd1-DBD / Type: protein / Description: chromodomain helicase DNA binding domain / Formula weight: 31.096 / Num. of mol.: 1 / Source: Saccharomyces cerevisiae / References: UniProt: P32657
Sequence:

RRARANDMDS IGESEVRALY KAILKFGNLK EILDELIADG TLPVKSFEKY GETYDEMMEA AKDCVHEEEK NRKEILEKLE KHATAYRAKL KSGEIKAENQ PKDNPLTRLS LKKREKKAVL FNFKGVKSLN AESLLSRVED LKYLKNLINS NYKDDPLKFS LGNNTPKPVQ NWSSNWTKEE DEKLLIGVFK YGYGSWTQIR DDPFLGITDK IFLNEVHNPV AKKSASSSDT TPTPSKKGKG ITGSSKKVPG AIHLGRRVDY LLSFLRGGLN TKSPSA

Experimental information

• Beam: Instrument name: DORIS III X33 / City: Hamburg / 国: Germany / Shape: 0.6 / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.154 Å / Dist. spec. to detc.: 5 mm
• Detector: Name: Pilatus 1M-W / Pixsize x: 0.172 mm

Scan

Title: DNA binding domain of S. cerevisiae Chromo domain- / Measurement date: Nov 20, 2009 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 30 sec. / Unit: 1/nm /

	Min	Max
Q	0.1201	6.237

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 1123 /

	Min	Max
Q	0.157483	3.15056
P(R) point	1	1123
R	0	8.39

Result

Type of curve: merged
Comments: The DNA binding module of Saccharomyces cerevisiae Chd1 protein.

	Experimental	Standard
MW	31.663 kDa	31.663 kDa

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	34.48	0.033	34.63	0.039
Radius of gyration, Rg	2.6 nm	0.003	2.6 nm	0.06

	Min	Max
D	-	8.3
Guinier point	1	143