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- PDB-8c58: CpG specific M.MpeI methyltransferase crystallized in the presenc... -

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Basic information

Entry
Database: PDB / ID: 8c58
TitleCpG specific M.MpeI methyltransferase crystallized in the presence of 5-hydroxycytosine and 5-methylcytosine containing dsDNA
Components
  • Cytosine-specific methyltransferase
  • DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(5OC)P*GP*CP*TP*GP*AP*A)-3')
  • DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)-3')
KeywordsTRANSFERASE / M.MpeI / DNA methyltransferase / DNA / 5-methylcytosine / 5-hydroxycytosine / 5mC / 5OHC / CpG
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / methylation
Similarity search - Function
: / DNA methylase, C-5 cytosine-specific, active site / C-5 cytosine-specific DNA methylases active site. / C-5 cytosine-specific DNA methylase (Dnmt) domain profile. / C-5 cytosine methyltransferase / C-5 cytosine-specific DNA methylase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
CARBONATE ION / S-ADENOSYLMETHIONINE / DNA / DNA (> 10) / Cytosine-specific methyltransferase
Similarity search - Component
Biological speciesMalacoplasma penetrans HF-2 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWojciechowski, M. / Czapinska, H. / Krwawicz, J. / Rafalski, D. / Bochtler, M.
Funding support Poland, European Union, 8items
OrganizationGrant numberCountry
Foundation for Polish ScienceTEAM/2010-6/1 Poland
European Union (EU)TEAM/2010-6/1European Union
Foundation for Polish SciencePOIR.04.04.00-00-31DF/17-00 Poland
European Union (EU)POIR.04.04.00-00-31DF/17-00European Union
Polish National Science CentreUMO-2014/13/B/NZ1/03991 Poland
Polish National Science CentreUMO-2014/14/M/NZ5/00558 Poland
Polish National Science CentreUMO-2018/30/Q/NZ2/00669 Poland
European Union (EU)POIG.02.02.00-14-024/08-00European Union
Citation
Journal: Nucleic Acids Res. / Year: 2024
Title: Cytosine analogues as DNA methyltransferase substrates.
Authors: Wojciechowski, M. / Czapinska, H. / Krwawicz, J. / Rafalski, D. / Bochtler, M.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013
Title: CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
Authors: Wojciechowski, M. / Czapinska, H. / Bochtler, M.
#2: Journal: Science / Year: 2012
Title: Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation.
Authors: Song, J. / Teplova, M. / Ishibe-Murakami, S. / Patel, D.J.
History
DepositionJan 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosine-specific methyltransferase
B: DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(5OC)P*GP*CP*TP*GP*AP*A)-3')
C: DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,02613
Polymers54,8313
Non-polymers1,19510
Water9,890549
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.521, 84.521, 172.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytosine-specific methyltransferase


Mass: 46238.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Malacoplasma penetrans HF-2 (bacteria) / Strain: HF-2 / Gene: MYPE4940 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): 2566 / References: UniProt: Q8EVR5

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(5OC)P*GP*CP*TP*GP*AP*A)-3')


Mass: 4265.782 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)-3')


Mass: 4325.829 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 4 types, 559 molecules

#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 294 K
Details: Since the pH of the crystallization drop (reservoir buffer pH 5.6) was close to the pK for the HCO3-/CO32-+H+ equilibrium (pKa=6.1), a mixture of carbonate and hydrogencarbonate is likely present in the crystal.
Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10% PEG 3350, 150 mM NaCl, 50 mM sodium citrate (final pH, 5.6). For cryoprotection glycerol was added to 25% v/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.2782 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2782 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. obs: 54230 / % possible obs: 99.5 % / Redundancy: 5.67 % / Biso Wilson estimate: 43.5 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.048 / Rsym value: 0.044 / Net I/σ(I): 21.76
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 5.66 % / Mean I/σ(I) obs: 1.97 / Num. unique obs: 8502 / CC1/2: 0.737 / Rrim(I) all: 1.067 / Rsym value: 0.967 / % possible all: 99

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
REFMACphasing
ARP/wARPmodel building
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DKJ

4dkj


Resolution: 1.85→19.95 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 6.808 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED SOLVENT MOLECULES HAVE BEEN MODELLED TENTATIVELY. S-ADENOSYLMETHIONINE (SAM) HAS BEEN MODELLED IN THE CO- ...Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES : WITH TLS ADDED SOLVENT MOLECULES HAVE BEEN MODELLED TENTATIVELY. S-ADENOSYLMETHIONINE (SAM) HAS BEEN MODELLED IN THE CO-SUBSTRATE BINDING POCKET BUT ONLY PARTS OF THE MOLECULE CORRESPONDING TO ITS BASE AND AMINO ACID END ARE RESOLVED IN THE ELECTRON DENSITY. THE CENTRAL PART OF THE CO-SUBSTRATE COULD NOT BE UNAMBIGUOUSLY TRACED, WHICH MAY BE DUE TO ITS DECOMPOSITION TO HOMOSERINE LACTONE (HSL) AND METHYLTHIOADENOSINE (MTA). THE RESIDUAL DIFFERENCE DENSITY NEXT TO THE SUBSTRATE BASE LIKELY RESULTS FROM THE RESIDUAL PRESENCE OF THE ACTIVE SITE LOOP IN THE "IN" CONFORMATION BUT THE OCCUPANCY OF THIS CONFORMER WAS TOO LOW TO BE INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 2689 5 %RANDOM
Rwork0.1648 ---
obs0.16626 51484 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.188 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å2-0 Å2
2--0.47 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 1.85→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 570 79 549 4305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0184303
X-RAY DIFFRACTIONr_bond_other_d0.0030.023880
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.865944
X-RAY DIFFRACTIONr_angle_other_deg0.8323.0019036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.735459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16225.412170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27215735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9591514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02988
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.972.9051728
X-RAY DIFFRACTIONr_mcbond_other0.972.9051728
X-RAY DIFFRACTIONr_mcangle_it1.6544.3422223
X-RAY DIFFRACTIONr_mcangle_other1.6544.3432224
X-RAY DIFFRACTIONr_scbond_it1.1033.1792575
X-RAY DIFFRACTIONr_scbond_other1.1033.1792575
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8844.713722
X-RAY DIFFRACTIONr_long_range_B_refined5.64436.7635679
X-RAY DIFFRACTIONr_long_range_B_other5.11334.6595348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å
RfactorNum. reflection% reflection
Rfree0.315 195 -
Rwork0.298 3656 -
obs--97.87 %
Refinement TLS params.Method: refined / Origin x: 23.063 Å / Origin y: 22.245 Å / Origin z: 45.811 Å
111213212223313233
T0.055 Å2-0.0349 Å2-0.001 Å2-0.138 Å20.0133 Å2--0.0019 Å2
L0.7487 °20.8455 °2-0.042 °2-1.8139 °20.3085 °2--0.7722 °2
S0.0793 Å °-0.1315 Å °-0.0096 Å °-0.0271 Å °-0.1031 Å °0.004 Å °-0.0294 Å °0.0857 Å °0.0238 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 395
2X-RAY DIFFRACTION1B1 - 14
3X-RAY DIFFRACTION1C1 - 14

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