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- PDB-4dkj: CpG specific methyltransferase in complex with target DNA -

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Basic information

Entry
Database: PDB / ID: 4dkj
TitleCpG specific methyltransferase in complex with target DNA
Components
  • Cytosine-specific methyltransferase
  • DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(C37)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/DNA / CG-SPECIFICITY / DNA INTERCALATION / CPG SEQUENCE / CYTOSINE C5-METHYLATION / C5-METHYLCYTOSINE / NUCLEOTIDE FLIPPING / S-adenosyl-L-methionine-dependent methyltransferases / C-5 cytosine-specific DNA methylases / DNA (cytosine-5-)-methyltransferase activity / DNA binding / DNA (cytosine-5-)-methylation / intracellular / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system
Similarity search - Function
DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / 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 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex ...DNA Methylase, subunit A, domain 2 / DNA Methylase; Chain A, domain 2 / 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 / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / Cytosine-specific methyltransferase
Similarity search - Component
Biological speciesMycoplasma penetrans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWojciechowski, M. / Czapinska, H. / Bochtler, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: CpG underrepresentation and the bacterial CpG-specific DNA methyltransferase M.MpeI.
Authors: Wojciechowski, M. / Czapinska, H. / Bochtler, M.
History
DepositionFeb 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Jan 16, 2013Group: Database references
Revision 1.4Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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*(C37)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)56,3805
Polymers55,9043
Non-polymers4772
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-21 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.950, 83.950, 173.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-785-

HOH

DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT CONTAINS PROTEIN CHAIN A, AND DNA STRANDS B AND C. THE TRIMER (ACCORDING TO PDB CONVENTIONS) IS A COMPLEX OF THE MONOMERIC METHYLTRANSFERASE WITH ITS SUBSTRATE, DOUBLE STRANDED DNA.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytosine-specific methyltransferase


Mass: 47310.082 Da / Num. of mol.: 1 / Mutation: S295P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma penetrans (bacteria) / Strain: HF-2 / Gene: MYPE4940 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q8EVR5, DNA (cytosine-5-)-methyltransferase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(C37)P*GP*CP*TP*GP*AP*A)-3')


Mass: 4267.773 Da / Num. of mol.: 1 / Source method: obtained synthetically
#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: obtained synthetically

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Non-polymers , 3 types, 269 molecules

#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THESE ARE NATURAL STRAIN VARIATIONS.

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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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 10% PEG 3350, 150 mM NaCl, 50 mM sodium. For cryoprotection glycerol was added to 25% v/v, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2010 / Details: BENT MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 34324 / Num. obs: 34324 / % possible obs: 99.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 5.5
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4957 / Rsym value: 0.31 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CHAINSAWmodel building
REFMACrefinement
ARP/wARPmodel building
MOSFLMdata reduction
SCALAdata scaling
CHAINSAWphasing
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C7P

2c7p


Resolution: 2.15→38.6 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: THROUGHOUT / ESU R: 0.214 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: (1) THE CRYSTAL WAS GROWN IN THE PRESENCE OF A SAMPLE THAT WAS LABELLED AS S-ADENOSYL-METHIONINE (SAM), BUT APPEARS TO HAVE BEEN DEGRADED TO S-ADENOSYL-HOMOCYSTEINE (SAH) EITHER PRIOR TO OR ...Details: (1) THE CRYSTAL WAS GROWN IN THE PRESENCE OF A SAMPLE THAT WAS LABELLED AS S-ADENOSYL-METHIONINE (SAM), BUT APPEARS TO HAVE BEEN DEGRADED TO S-ADENOSYL-HOMOCYSTEINE (SAH) EITHER PRIOR TO OR DURING CRYSTALLIZATION. PROGRAM CNS HAS BEEN USED FOR DNA REFINEMENT. NO SUGAR PUCKER CONSTRAINTS HAVE BEEN APPLIED. (2) THE MODELLED S-ADENOSYLHOMOCYSTEINE (SAH) IS UNCERTAIN. ITS BINDING SITE MIGHT BE OCCUPIED IN PART BY S-ADENOSYLMETHIONINE (SAM) OR THE SAM DEGRADATION PRODUCT 5 -METHYLTHIOADENOSINE (MTA) (FROM SCISSION OF SAM TO MTA AND HOMOSERINE LACTONE). THE DISTANCE BETWEEN CYS135 S AND C6 OF THE SUBSTRATE CYTOSINE BASE IS INTERMEDIATE BETWEEN A NON-COVALENT AND A COVALENT BOND. A DISTANCE BELOW THE VAN DER WAALS LIMIT SUGGESTS THAT SLIGHT DEVIATIONS FROM THE PLANARITY OF THE DNA BASE SHOULD OCCUR. AS THE RESOLUTION OF THE X-RAY DATA IS INSUFFICIENT TO DETECT SUCH DEVIATIONS, THEY WERE NOT MODELLED. (3) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21631 1729 5 %RANDOM
Rwork0.17632 ---
all0.17832 34274 --
obs0.17832 34274 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.15→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3199 570 32 267 4068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224388
X-RAY DIFFRACTIONr_bond_other_d00.022941
X-RAY DIFFRACTIONr_angle_refined_deg1.2532.1316064
X-RAY DIFFRACTIONr_angle_other_deg3.96637256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.165471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25425.301183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06315767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2091517
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024548
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02810
X-RAY DIFFRACTIONr_nbd_refined0.1920.2771
X-RAY DIFFRACTIONr_nbd_other0.2320.22985
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22059
X-RAY DIFFRACTIONr_nbtor_other0.1080.21868
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2258
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0790.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.380.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 138 -
Rwork0.203 2348 -
obs-2486 99.92 %
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)
11.32850.71390.08991.83040.2161.4460.1138-0.20950.15970.0245-0.09820.065-0.17030.1231-0.0156-0.0916-0.06680.0118-0.0382-0.023-0.085725.87530.82349.244
20.97240.6691-0.19992.20690.04680.7196-0.0188-0.0366-0.0063-0.1209-0.05620.12950.0652-0.07670.0749-0.0695-0.0421-0.0339-0.01850.0294-0.02612.6019.25640.543
31.3002-0.07890.43931.9057-0.02692.10450.1105-0.0305-0.0781-0.01290.0146-0.24260.13460.3025-0.1251-0.05030.01550.00140.00550.0614-0.022729.065.7643.562
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 259
2X-RAY DIFFRACTION1A376 - 393
3X-RAY DIFFRACTION2A260 - 375
4X-RAY DIFFRACTION3B1 - 14
5X-RAY DIFFRACTION3C1 - 14

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