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- PDB-1ugh: CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 1ugh
TitleCRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE IN COMPLEX WITH A PROTEIN INHIBITOR: PROTEIN MIMICRY OF DNA
Components
  • PROTEIN (URACIL-DNA GLYCOSYLASE INHIBITOR)
  • PROTEIN (URACIL-DNA GLYCOSYLASE)
KeywordsGLYCOSYLASE / ENZYME-INHIBITOR COMPLEX
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine ...base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / depyrimidination / Displacement of DNA glycosylase by APEX1 / isotype switching / uracil DNA N-glycosylase activity / ribosomal small subunit binding / somatic hypermutation of immunoglobulin genes / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Chromatin modifications during the maternal to zygotic transition (MZT) / base-excision repair / damaged DNA binding / negative regulation of apoptotic process / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E ...Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase family 1 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase / Uracil-DNA glycosylase inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
Bacillus phage PBS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMol, C.D. / Arvai, A.S. / Sanderson, R.J. / Slupphaug, G. / Kavli, B. / Krokan, H.E. / Mosbaugh, D.W. / Tainer, J.A.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA.
Authors: Mol, C.D. / Arvai, A.S. / Sanderson, R.J. / Slupphaug, G. / Kavli, B. / Krokan, H.E. / Mosbaugh, D.W. / Tainer, J.A.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase.
Authors: Putnam, C.D. / Shroyer, M.J. / Lundquist, A.J. / Mol, C.D. / Arvai, A.S. / Mosbaugh, D.W. / Tainer, J.A.
#2: Journal: Embo J. / Year: 1998
Title: Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.
Authors: Parikh, S.S. / Mol, C.D. / Slupphaug, G. / Bharati, S. / Krokan, H.E. / Tainer, J.A.
#3: Journal: Nature / Year: 1996
Title: A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.
Authors: Slupphaug, G. / Mol, C.D. / Kavli, B. / Arvai, A.S. / Krokan, H.E. / Tainer, J.A.
#4: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis.
Authors: Mol, C.D. / Arvai, A.S. / Slupphaug, G. / Kavli, B. / Alseth, I. / Krokan, H.E. / Tainer, J.A.
History
DepositionFeb 5, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Aug 23, 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

Downloads & links

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Assembly

Deposited unit
E: PROTEIN (URACIL-DNA GLYCOSYLASE)
I: PROTEIN (URACIL-DNA GLYCOSYLASE INHIBITOR)


Theoretical massNumber of molelcules
Total (without water)34,7952
Polymers34,7952
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-11 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.320, 64.690, 55.340
Angle α, β, γ (deg.)90.00, 113.77, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein PROTEIN (URACIL-DNA GLYCOSYLASE) / EC 3.2.2.3 / UDG


Mass: 25544.137 Da / Num. of mol.: 1 / Mutation: P82M, V83E, G84F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P13051, uridine nucleosidase
#2: Protein PROTEIN (URACIL-DNA GLYCOSYLASE INHIBITOR) / UGI


Mass: 9250.373 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage PBS2 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P14739
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growpH: 5 / Details: pH 5.0
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2IMIDAZOLE/MALEATE BUFFER11
3PEG 400012
4IMIDAZOLE/MALEATE BUFFER12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
220 %PEG40001reservoir
3100 mMimidazole/malate1reservoir
41

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.9→8 Å / Num. obs: 21979 / % possible obs: 90 % / Redundancy: 1.92 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.047 / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→1.97 Å / Rsym value: 0.224 / % possible all: 76
Reflection
*PLUS
Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 76 % / Rmerge(I) obs: 0.224

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AKZ

1akz


Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 3
Details: UGI RESIDUES MET1 AND THR2 ARE DISORDERED AND NOT SEEN IN THE ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2190 10 %RANDOM
Rwork0.198 ---
obs-17752 72.8 %-
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-15.7 Å20 Å20 Å2
2---2.41 Å20 Å2
3---7.927 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 0 185 2640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.385
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.91
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3951 140 4.6 %
Rwork0.3394 1126 -
obs--41.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.91
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27
LS refinement shell
*PLUS
Rfactor obs: 0.3394

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