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- PDB-1akz: HUMAN URACIL-DNA GLYCOSYLASE -

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Basic information

Entry
Database: PDB / ID: 1akz
TitleHUMAN URACIL-DNA GLYCOSYLASE
ComponentsURACIL-DNA GLYCOSYLASE
KeywordsGLYCOSIDASE / GLYCOSYLASE / DNA REPAIR / URACIL REMOVAL FROM DNA / ALPHA/ BETA PROTEIN
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
Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.57 Å
AuthorsTainer, J.A. / Mol, C.D.
CitationJournal: 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.
History
DepositionMay 27, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: URACIL-DNA GLYCOSYLASE


Theoretical massNumber of molelcules
Total (without water)25,5441
Polymers25,5441
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.760, 55.270, 84.970
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 URACIL-DNA GLYCOSYLASE / / UDG / UNG


Mass: 25544.137 Da / Num. of mol.: 1 / Mutation: P82M, V83E, G84F
Source method: isolated from a genetically manipulated source
Details: STRUCTURE IS THAT OF RECOMBINANT HUMAN URACIL-DNA GLYCOSYLASE IN WHICH THE 84 N-TERMINAL AMINO ACIDS CODED FOR BY THE UNG GENE HAVE BEEN REPLACED BY THREE RESIDUES FROM THE EXPRESSION VECTOR
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P13051, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Water ChemComp-HOH / water / 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: 2.25 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.9
Details: 100 MM IMIDAZOLE/MALEATE, PH 7.9, 1%-4% SATURATED NACL, 1%-4% SATURATED AMMONIUM SULFATE, 16%-20% PEG 4000, MIXED WITH EQUAL VOLUMES 30 MG/ML PROTEIN.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Mol, C.D., (1995) Cell. 80, 869.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
216-20 %PEG40001reservoir
3100 mMimidazole/malate1reservoirpH7.9
41-4 %sat1reservoirNaCl
51-4 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorDate: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 30433 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.9
Reflection shellResolution: 1.57→1.61 Å / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 11 / % possible all: 93.4
Reflection
*PLUS
Num. obs: 30415 / Num. measured all: 121341
Reflection shell
*PLUS
% possible obs: 93.3 % / Rmerge(I) obs: 0.103

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Processing

Software
NameVersionClassification
PHASESphasing
SQUASHphasing
XTALVIEWrefinement
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.57→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: AN OVERALL BULK SOLVENT CORRECTION WAS APPLIED TO THE DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3048 9.49 %RANDOM
Rwork0.189 ---
obs0.189 30381 94.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9022 Å20 Å20 Å2
2--0.7885 Å20 Å2
3----5.6908 Å2
Refinement stepCycle: LAST / Resolution: 1.57→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 0 185 1993
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.154
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.96
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.949
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.9581.5
X-RAY DIFFRACTIONx_mcangle_it1.6492
X-RAY DIFFRACTIONx_scbond_it1.7462
X-RAY DIFFRACTIONx_scangle_it2.8122.5
LS refinement shellResolution: 1.57→1.64 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.286 390 9.85 %
Rwork0.318 3319 -
obs--93.7 %
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: 3.8 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 29891 / Rfactor obs: 0.187 / Rfactor Rfree: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.96
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.949
LS refinement shell
*PLUS
Rfactor obs: 0.318

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