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- PDB-5yy9: Crystal structure of Tandem Tudor Domain of human UHRF1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5yy9
TitleCrystal structure of Tandem Tudor Domain of human UHRF1 in complex with LIG1-K126me3
Components
  • E3 ubiquitin-protein ligase UHRF1
  • Ligase 1
KeywordsTRANSFERASE / Maintenance of DNA methylation
Function / homology
Function and homology information


Okazaki fragment processing involved in mitotic DNA replication / histone H3 ubiquitin ligase activity / DNA ligase activity / DNA damage sensor activity / DNA ligase (ATP) / hemi-methylated DNA-binding / DNA ligase (ATP) activity / homologous recombination / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Processive synthesis on the lagging strand ...Okazaki fragment processing involved in mitotic DNA replication / histone H3 ubiquitin ligase activity / DNA ligase activity / DNA damage sensor activity / DNA ligase (ATP) / hemi-methylated DNA-binding / DNA ligase (ATP) activity / homologous recombination / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / Processive synthesis on the lagging strand / regulation of epithelial cell proliferation / lagging strand elongation / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / methyl-CpG binding / histone H3K9me2/3 reader activity / DNA biosynthetic process / negative regulation of gene expression via chromosomal CpG island methylation / Early Phase of HIV Life Cycle / : / positive regulation of protein metabolic process / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / anatomical structure morphogenesis / mitotic spindle assembly / mismatch repair / heterochromatin / protein autoubiquitination / cis-regulatory region sequence-specific DNA binding / base-excision repair, gap-filling / epigenetic regulation of gene expression / DNA methylation / Gap-filling DNA repair synthesis and ligation in GG-NER / replication fork / Chromatin modifications during the maternal to zygotic transition (MZT) / euchromatin / double-strand break repair via homologous recombination / base-excision repair / RING-type E3 ubiquitin transferase / spindle / nuclear matrix / Gap-filling DNA repair synthesis and ligation in TC-NER / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / heterochromatin formation / ubiquitin-dependent protein catabolic process / DNA recombination / histone binding / nucleic acid binding / protein ubiquitination / cell division / DNA repair / intracellular membrane-bounded organelle / DNA damage response / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus
Similarity search - Function
: / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. ...: / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / SH3 type barrels. - #30 / PUA-like superfamily / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / SH3 type barrels. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Roll / Ubiquitin-like domain superfamily / Nucleic acid-binding, OB-fold / Mainly Beta
Similarity search - Domain/homology
DNA ligase 1 / E3 ubiquitin-protein ligase UHRF1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.653 Å
AuthorsKori, S. / Defossez, P.A. / Arita, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSTPRESTO 14530337 Japan
CitationJournal: Structure / Year: 2019
Title: Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation.
Authors: Kori, S. / Ferry, L. / Matano, S. / Jimenji, T. / Kodera, N. / Tsusaka, T. / Matsumura, R. / Oda, T. / Sato, M. / Dohmae, N. / Ando, T. / Shinkai, Y. / Defossez, P.A. / Arita, K.
History
DepositionDec 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / 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
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Nov 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: E3 ubiquitin-protein ligase UHRF1
B: E3 ubiquitin-protein ligase UHRF1
C: Ligase 1
D: Ligase 1


Theoretical massNumber of molelcules
Total (without water)39,6054
Polymers39,6054
Non-polymers00
Water43224
1
A: E3 ubiquitin-protein ligase UHRF1
C: Ligase 1


Theoretical massNumber of molelcules
Total (without water)19,8022
Polymers19,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-4 kcal/mol
Surface area9240 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase UHRF1
D: Ligase 1


Theoretical massNumber of molelcules
Total (without water)19,8022
Polymers19,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-5 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.105, 97.349, 132.529
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase UHRF1 / Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein ...Inverted CCAAT box-binding protein of 90 kDa / Nuclear protein 95 / Nuclear zinc finger protein Np95 / hNp95 / RING finger protein 106 / RING-type E3 ubiquitin transferase UHRF1 / Transcription factor ICBP90 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / hUHRF1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 18162.207 Da / Num. of mol.: 2 / Fragment: Tandem Tudor Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UHRF1, ICBP90, NP95, RNF106 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q96T88, RING-type E3 ubiquitin transferase
#2: Protein/peptide Ligase 1


Mass: 1640.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P18858*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 00 mM Tris-HCl (pH 7.0), 200 mM tri-potassium phosphate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.65→48.67 Å / Num. obs: 40019 / % possible obs: 97 % / Redundancy: 3.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.5
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.95 / % possible all: 95.4

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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: 3DB3

3db3


Resolution: 2.653→40.228 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.67
RfactorNum. reflection% reflection
Rfree0.2877 1034 9.97 %
Rwork0.2309 --
obs0.2367 10370 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.653→40.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 0 24 2414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042435
X-RAY DIFFRACTIONf_angle_d0.8123304
X-RAY DIFFRACTIONf_dihedral_angle_d21.6511464
X-RAY DIFFRACTIONf_chiral_restr0.053360
X-RAY DIFFRACTIONf_plane_restr0.006429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6535-2.79340.38011340.30681269X-RAY DIFFRACTION94
2.7934-2.96830.39261560.29991327X-RAY DIFFRACTION98
2.9683-3.19740.33441480.2771315X-RAY DIFFRACTION98
3.1974-3.5190.28781430.24231330X-RAY DIFFRACTION96
3.519-4.02780.23991620.22171334X-RAY DIFFRACTION97
4.0278-5.0730.2431330.17761344X-RAY DIFFRACTION95
5.073-40.23260.30011580.22331417X-RAY DIFFRACTION94

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