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- PDB-2mwi: The structure of the carboxy-terminal domain of DNTTIP1 -

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Basic information

Entry
Database: PDB / ID: 2mwi
TitleThe structure of the carboxy-terminal domain of DNTTIP1
ComponentsDeoxynucleotidyltransferase terminal-interacting protein 1
KeywordsPROTEIN BINDING / HDAC / histone deacetylase / gene expression / DNTTIP1 / MIDEAS / HDAC1 / TDIF1
Function / homology
Function and homology information


histone deacetylase complex / nucleosome binding / chromosome / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Terminal deoxynucleotidyltransferase-interacting factor 1 / DNTTIP1, dimerisation domain / : / DNTTIP1 dimerisation domain / TdIF1, C-terminal
Similarity search - Domain/homology
Deoxynucleotidyltransferase terminal-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSchwabe, J.W.R. / Muskett, F.W. / Itoh, T.
CitationJournal: Nucleic Acids Res / Year: 2015
Title: Structural and functional characterization of a cell cycle associated HDAC1/2 complex reveals the structural basis for complex assembly and nucleosome targeting.
Authors: Toshimasa Itoh / Louise Fairall / Frederick W Muskett / Charles P Milano / Peter J Watson / Nadia Arnaudo / Almutasem Saleh / Christopher J Millard / Mohammed El-Mezgueldi / Fabrizio Martino ...Authors: Toshimasa Itoh / Louise Fairall / Frederick W Muskett / Charles P Milano / Peter J Watson / Nadia Arnaudo / Almutasem Saleh / Christopher J Millard / Mohammed El-Mezgueldi / Fabrizio Martino / John W R Schwabe /
Abstract: Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and ...Recent proteomic studies have identified a novel histone deacetylase complex that is upregulated during mitosis and is associated with cyclin A. This complex is conserved from nematodes to man and contains histone deacetylases 1 and 2, the MIDEAS corepressor protein and a protein called DNTTIP1 whose function was hitherto poorly understood. Here, we report the structures of two domains from DNTTIP1. The amino-terminal region forms a tight dimerization domain with a novel structural fold that interacts with and mediates assembly of the HDAC1:MIDEAS complex. The carboxy-terminal domain of DNTTIP1 has a structure related to the SKI/SNO/DAC domain, despite lacking obvious sequence homology. We show that this domain in DNTTIP1 mediates interaction with both DNA and nucleosomes. Thus, DNTTIP1 acts as a dimeric chromatin binding module in the HDAC1:MIDEAS corepressor complex.
History
DepositionNov 11, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxynucleotidyltransferase terminal-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)14,0601
Polymers14,0601
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)65 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Deoxynucleotidyltransferase terminal-interacting protein 1 / Terminal deoxynucleotidyltransferase-interacting factor 1 / TdIF1 / TdT-interacting factor 1


Mass: 14060.202 Da / Num. of mol.: 1 / Fragment: carboxy-terminal domain (UNP residues 197-316)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNTTIP1, C20orf167, TDIF1 / Plasmid: pET30A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS / References: UniProt: Q9H147

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HN(CO)CA
1513D HNHA
1613D HBHA(CO)NH
1713D HNCA
1813D HNCO
2923D (H)CCH-TOCSY
21023D CCH-TOCSY
21122D 1H-13C HSQC
11213D 1H-15N NOESY
21323D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-100% 13C; U-100% 15N] DNTTIP1(197-316), 40 mM potassium phosphate, 1 mM DTT, 1 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.3 mM [U-100% 13C; U-100% 15N] DNTTIP1(197-316), 40 mM potassium phosphate, 1 mM DTT, 1 mM sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMDNTTIP1(197-316)-1[U-100% 13C; U-100% 15N]1
40 mMpotassium phosphate-21
1 mMDTT-31
1 mMsodium azide-41
0.3 mMDNTTIP1(197-316)-5[U-100% 13C; U-100% 15N]2
40 mMpotassium phosphate-62
1 mMDTT-72
1 mMsodium azide-82
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
180 6.0 ambient 298 K
280 6.0 ambient 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker AvanceBrukerAvance8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
SPARKY3.1Goddardchemical shift assignment
TOPSPIN2.1Bruker Biospincollection
TOPSPIN2.1Bruker Biospinprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 65

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