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- PDB-5wy1: Crystal structure of mouse DNA methyltransferase 1 (T1505A mutant) -

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Basic information

Entry
Database: PDB / ID: 5wy1
TitleCrystal structure of mouse DNA methyltransferase 1 (T1505A mutant)
ComponentsDNA (cytosine-5)-methyltransferase 1
KeywordsTRANSFERASE / CpG sequence / mutant / epigenetics / hemimethylated DNA
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
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 / DMAP1-binding domain / DMAP1-binding domain profile. / 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 ...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 / DMAP1-binding domain / DMAP1-binding domain profile. / 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. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
DNA (cytosine-5)-methyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsKanada, K. / Takeshita, K. / Suetake, I. / Tajima, S. / Nakagawa, A.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP23770145 Japan
Japan Science and Technology Agency Japan
Japan Society for the Promotion of ScienceJP24570153 Japan
Japan Society for the Promotion of ScienceJP22370053 Japan
Japan Society for the Promotion of Science/the Ministry of Education, Culture, Sports, Science and TechnologyJP 25291025 Japan
the National Project on Protein Structural and Functional Analyses Japan
CitationJournal: J. Biochem. / Year: 2017
Title: Conserved threonine 1505 in the catalytic domain stabilizes mouse DNA methyltransferase 1
Authors: Kanada, K. / Takeshita, K. / Suetake, I. / Tajima, S. / Nakagawa, A.
History
DepositionJan 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)151,0285
Polymers150,7661
Non-polymers2624
Water41423
1
A: DNA (cytosine-5)-methyltransferase 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)302,05610
Polymers301,5332
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)134.998, 97.804, 130.319
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 150766.438 Da / Num. of mol.: 1 / Fragment: UNP residues 29-1620 / Mutation: T1505A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dnmt1, Dnmt, Met1, Uim / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P13864, DNA (cytosine-5-)-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 3350, NaCl, TCEP, Na-citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.26→50 Å / Num. obs: 26720 / % possible obs: 97.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 73.5 Å2 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.106 / Rrim(I) all: 0.219 / Χ2: 0.943 / Net I/av σ(I): 6.612 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.26-3.324.40.7480.355196.4
3.32-3.384.40.6370.377196.4
3.38-3.444.50.6030.448196.2
3.44-3.514.40.5390.589196.6
3.51-3.594.50.4840.668196.7
3.59-3.674.50.4240.738197.4
3.67-3.764.50.340.795197.3
3.76-3.864.50.3370.822197.9
3.86-3.984.50.2810.862198.2
3.98-4.114.50.240.916198.6
4.11-4.254.50.210.916198.5
4.25-4.424.50.1510.96199
4.42-4.634.50.130.966199.1
4.63-4.874.40.1160.971199.2
4.87-5.174.50.1080.973198.9
5.17-5.574.50.1060.974198.9
5.57-6.134.50.0970.98198.4
6.13-7.024.50.0770.988197.4
7.02-8.834.40.0590.991196.8
8.83-504.10.0490.992192.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
Cootmodel building
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AV4

3av4


Resolution: 3.27→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.874 / SU B: 59.92 / SU ML: 0.428 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.562
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 1255 5.1 %RANDOM
Rwork0.2032 ---
obs0.2061 23536 90.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 181.98 Å2 / Biso mean: 87.666 Å2 / Biso min: 38.58 Å2
Baniso -1Baniso -2Baniso -3
1--3.31 Å20 Å20 Å2
2---1.97 Å20 Å2
3---5.28 Å2
Refinement stepCycle: final / Resolution: 3.27→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9108 0 4 23 9135
Biso mean--74.32 62.65 -
Num. residues----1140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199328
X-RAY DIFFRACTIONr_bond_other_d0.0010.028735
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.95912612
X-RAY DIFFRACTIONr_angle_other_deg2.311320153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20451129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59923.797453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.858151600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0641568
X-RAY DIFFRACTIONr_chiral_restr0.0740.21335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110546
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022190
X-RAY DIFFRACTIONr_mcbond_it3.7736.6124549
X-RAY DIFFRACTIONr_mcbond_other3.7686.6124548
X-RAY DIFFRACTIONr_mcangle_it6.2529.9025667
LS refinement shellResolution: 3.266→3.351 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 53 -
Rwork0.269 1025 -
all-1078 -
obs--54.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.51140.0230.53830.61850.12051.10310.1483-0.0821-0.02180.1535-0.0215-0.10810.1356-0.0715-0.12680.1446-0.0573-0.0430.02660.01180.039478.083926.462832.1766
20.72110.4243-0.06480.2782-0.09640.8848-0.08060.25390.313-0.0720.21130.21370.18430.1843-0.13070.4005-0.1034-0.18160.38670.12690.235173.951722.958625.7921
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A357 - 1612
2X-RAY DIFFRACTION1A2001 - 2004
3X-RAY DIFFRACTION2A2101 - 2123

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