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- PDB-1u2z: Crystal structure of histone K79 methyltransferase Dot1p from yeast -

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Basic information

Entry
Database: PDB / ID: 1u2z
TitleCrystal structure of histone K79 methyltransferase Dot1p from yeast
ComponentsHistone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
KeywordsTRANSFERASE / Histone methyltransferase / Nucleosome
Function / homology
Function and homology information


negative regulation of heterochromatin formation / meiotic recombination checkpoint signaling / : / histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / global genome nucleotide-excision repair / recombinational repair / postreplication repair / mitotic intra-S DNA damage checkpoint signaling ...negative regulation of heterochromatin formation / meiotic recombination checkpoint signaling / : / histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / global genome nucleotide-excision repair / recombinational repair / postreplication repair / mitotic intra-S DNA damage checkpoint signaling / subtelomeric heterochromatin formation / mitotic G1 DNA damage checkpoint signaling / DNA damage checkpoint signaling / nucleotide-excision repair / nucleosome assembly / nucleosome / histone binding / chromosome, telomeric region / DNA repair / DNA binding / nucleus
Similarity search - Function
434 Repressor (Amino-terminal Domain) - #170 / Histone H3-K79 methyltransferase, fungi / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / 434 Repressor (Amino-terminal Domain) / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold ...434 Repressor (Amino-terminal Domain) - #170 / Histone H3-K79 methyltransferase, fungi / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / 434 Repressor (Amino-terminal Domain) / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsSawada, K. / Yang, Z. / Horton, J.R. / Collins, R.E. / Zhang, X. / Cheng, X.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase
Authors: Sawada, K. / Yang, Z. / Horton, J.R. / Collins, R.E. / Zhang, X. / Cheng, X.
History
DepositionJul 20, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Histone-lysine N-methyltransferase, H3 lysine-79 specific
B: Histone-lysine N-methyltransferase, H3 lysine-79 specific
C: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,8556
Polymers149,7023
Non-polymers1,1533
Water9,602533
1
A: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2852
Polymers49,9011
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2852
Polymers49,9011
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone-lysine N-methyltransferase, H3 lysine-79 specific
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2852
Polymers49,9011
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.070, 146.275, 75.412
Angle α, β, γ (deg.)90.00, 97.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-lysine N-methyltransferase, H3 lysine-79 specific / Histone methyltransferase / Histone H3-K79 methyltransferase / H3-K79-HMTase / Disrupter of telomere silencing protein 1


Mass: 49900.750 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DOT1 / Plasmid: pXC415 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q04089, histone-lysine N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.7 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, Glycerol, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 2, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 79720 / Num. obs: 79720 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 23.2
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 4.1 / Num. unique all: 7581 / % possible all: 94.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1019720.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3958 5 %RANDOM
Rwork0.213 ---
obs0.213 78422 98.9 %-
all-78422 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.2914 Å2 / ksol: 0.353296 e/Å3
Displacement parametersBiso mean: 46.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0.77 Å2
2--4.9 Å20 Å2
3----4.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9298 0 78 533 9909
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 641 5.1 %
Rwork0.272 12051 -
obs-11971 96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3SAM.PARAM
X-RAY DIFFRACTION4DNA-RNA_REP.PARAM
X-RAY DIFFRACTION5ION.PARAM

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