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- PDB-5gut: The crystal structure of mouse DNMT1 (731-1602) mutant - N1248A -

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Basic information

Entry
Database: PDB / ID: 5gut
TitleThe crystal structure of mouse DNMT1 (731-1602) mutant - N1248A
ComponentsDNA (cytosine-5)-methyltransferase 1
KeywordsTRANSFERASE / Mutant
Function / homology
Function and homology information


SUMOylation of DNA methylation proteins / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / : / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / PRC2 methylates histones and DNA / : / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity ...SUMOylation of DNA methylation proteins / negative regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / : / DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates / PRC2 methylates histones and DNA / : / epigenetic programming of gene expression / cellular response to bisphenol A / negative regulation of vascular associated smooth muscle cell apoptotic process / DNA-methyltransferase activity / S-adenosylmethionine metabolic process / DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA methylation-dependent heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / female germ cell nucleus / methyl-CpG binding / germ cell nucleus / : / heterochromatin / pericentric heterochromatin / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to transforming growth factor beta stimulus / replication fork / methyltransferase activity / nuclear estrogen receptor binding / promoter-specific chromatin binding / cellular response to amino acid stimulus / histone deacetylase binding / regulation of cell population proliferation / regulation of gene expression / response to xenobiotic stimulus / protein domain specific binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Bromo adjacent homology (BAH) domain / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DNA Methylase, subunit A, domain 2 / DMAP1-binding domain / DMAP1-binding domain profile. / DNA Methylase; Chain A, domain 2 ...Bromo adjacent homology (BAH) domain / DNA (cytosine-5)-methyltransferase 1-like / DNA (cytosine-5)-methyltransferase 1, replication foci domain / Cytosine specific DNA methyltransferase replication foci domain / DMAP1-binding Domain / DMAP1-binding Domain / DNA Methylase, subunit A, domain 2 / DMAP1-binding domain / DMAP1-binding domain profile. / DNA Methylase; Chain A, domain 2 / DNA methylase, C-5 cytosine-specific, conserved site / C-5 cytosine-specific DNA methylases C-terminal signature. / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Vaccinia Virus protein VP39 / SH3 type barrels. / Roll / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsChen, S.J. / Ye, F.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China81402849 China
National Natural Science Foundation of China21472208 China
National Natural Science Foundation of China21210003 China
CitationJournal: ACS Chem. Biol. / Year: 2018
Title: Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1.
Authors: Ye, F. / Kong, X. / Zhang, H. / Liu, Y. / Shao, Z. / Jin, J. / Cai, Y. / Zhang, R. / Li, L. / Zhang, Y.W. / Liu, Y.C. / Zhang, C. / Xie, W. / Yu, K. / Ding, H. / Zhao, K. / Chen, S. / Jiang, ...Authors: Ye, F. / Kong, X. / Zhang, H. / Liu, Y. / Shao, Z. / Jin, J. / Cai, Y. / Zhang, R. / Li, L. / Zhang, Y.W. / Liu, Y.C. / Zhang, C. / Xie, W. / Yu, K. / Ding, H. / Zhao, K. / Chen, S. / Jiang, H. / Baylin, S.B. / Luo, C.
History
DepositionAug 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (cytosine-5)-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,32614
Polymers98,8501
Non-polymers1,47613
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-26 kcal/mol
Surface area36890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.424, 78.554, 164.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA (cytosine-5)-methyltransferase 1 / Met-1 / DNA methyltransferase MmuI / M.MmuI / MCMT


Mass: 98850.453 Da / Num. of mol.: 1 / Fragment: UNP residues 731-1602 / Mutation: N1248A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt1, Dnmt, Met1, Uim / Plasmid: pET28a / Details (production host): His SUMO Tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: P13864, DNA (cytosine-5-)-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Lithium sulfate monohydrate, 0.1M Tris hydrochloride pH 8.5, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Dec 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.099→44.36 Å / Num. obs: 57583 / % possible obs: 97 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.1071 / Net I/σ(I): 22.28
Reflection shellResolution: 2.099→2.174 Å / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PT9

3pt9


Resolution: 2.099→44.36 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.09
RfactorNum. reflection% reflection
Rfree0.2305 2719 4.86 %
Rwork0.1996 --
obs0.2011 55932 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.099→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6366 0 78 479 6923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126645
X-RAY DIFFRACTIONf_angle_d1.6569015
X-RAY DIFFRACTIONf_dihedral_angle_d26.7452483
X-RAY DIFFRACTIONf_chiral_restr0.103940
X-RAY DIFFRACTIONf_plane_restr0.0121171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0991-2.13730.28421150.24262231X-RAY DIFFRACTION78
2.1373-2.17840.26691090.2362354X-RAY DIFFRACTION82
2.1784-2.22290.26411670.23192681X-RAY DIFFRACTION95
2.2229-2.27120.25651520.23832767X-RAY DIFFRACTION97
2.2712-2.3240.27531370.23012806X-RAY DIFFRACTION98
2.324-2.38210.25511180.22642837X-RAY DIFFRACTION99
2.3821-2.44650.27791380.2282854X-RAY DIFFRACTION99
2.4465-2.51850.27271420.22332860X-RAY DIFFRACTION99
2.5185-2.59980.25091660.21782851X-RAY DIFFRACTION100
2.5998-2.69270.24051530.20662848X-RAY DIFFRACTION99
2.6927-2.80050.24791200.19872791X-RAY DIFFRACTION96
2.8005-2.92790.22791630.19762853X-RAY DIFFRACTION99
2.9279-3.08230.24581480.19692877X-RAY DIFFRACTION100
3.0823-3.27530.22831710.19562881X-RAY DIFFRACTION99
3.2753-3.52810.22741400.18372897X-RAY DIFFRACTION100
3.5281-3.8830.21491200.17152934X-RAY DIFFRACTION99
3.883-4.44450.1961620.17142865X-RAY DIFFRACTION98
4.4445-5.5980.20091690.17912946X-RAY DIFFRACTION100
5.598-45.39120.21751290.21873080X-RAY DIFFRACTION98

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