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- PDB-5guv: The crystal structure of mouse DNMT1 (731-1602) mutant - R1279D -

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Basic information

Entry
Database: PDB / ID: 5guv
TitleThe crystal structure of mouse DNMT1 (731-1602) mutant - R1279D
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
DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.078 Å
AuthorsYe, F. / Chen, S.J.
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.Q. / 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. / ...Authors: Ye, F. / Kong, X.Q. / 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 1.0Aug 30, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,9823
Polymers98,8511
Non-polymers1312
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.039, 79.039, 393.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 98851.367 Da / Num. of mol.: 1 / Fragment: UNP residues 731-1602 / Mutation: R1279D
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) RI
References: UniProt: P13864, DNA (cytosine-5-)-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.11 Å3/Da / Density % sol: 60.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 25% (w/v) PEG 1500, 100mM SPG, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.078→61.602 Å / Num. obs: 24332 / % possible obs: 99 % / Redundancy: 27.8 % / Net I/σ(I): 17.64

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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: 3.078→61.602 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9
RfactorNum. reflection% reflection
Rfree0.268 1233 5.13 %
Rwork0.214 --
obs0.2168 24047 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.078→61.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6479 0 2 61 6542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136652
X-RAY DIFFRACTIONf_angle_d1.8049029
X-RAY DIFFRACTIONf_dihedral_angle_d20.3172450
X-RAY DIFFRACTIONf_chiral_restr0.101954
X-RAY DIFFRACTIONf_plane_restr0.0111187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0782-3.20150.3351330.25412475X-RAY DIFFRACTION99
3.2015-3.34720.30641220.24432484X-RAY DIFFRACTION99
3.3472-3.52360.27641380.23772492X-RAY DIFFRACTION99
3.5236-3.74440.35961430.22812494X-RAY DIFFRACTION99
3.7444-4.03340.2631190.21872507X-RAY DIFFRACTION99
4.0334-4.43920.26361550.19822510X-RAY DIFFRACTION99
4.4392-5.08130.20591350.1862535X-RAY DIFFRACTION99
5.0813-6.40080.25021460.20992569X-RAY DIFFRACTION99
6.4008-61.61390.24711420.20492748X-RAY DIFFRACTION97

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