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- PDB-4skn: A NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACI... -

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Basic information

Entry
Database: PDB / ID: 4skn
TitleA NUCLEOTIDE-FLIPPING MECHANISM FROM THE STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO DNA
Components
  • DNA (5'-D(*AP*AP*AP*GP*CP*CP*GP*CP*CP*C)-3')
  • DNA (5'-D(*TP*GP*GP*GP*(D1P)P*GP*GP*CP*TP*T)-3')
  • PROTEIN (URACIL-DNA GLYCOSYLASE)
KeywordsHYDROLASE/DNA / DNA GLYCOSYLASE / DNA BASE EXCISION REPAIR / URACIL / DNA / HYDROLASE-DNA 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
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 ...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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URACIL / DNA / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSlupphaug, G. / Mol, C.D. / Kavli, B. / Arvai, A.S. / Krokan, H.E. / Tainer, J.A.
CitationJournal: 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.
History
DepositionFeb 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*GP*GP*GP*(D1P)P*GP*GP*CP*TP*T)-3')
B: DNA (5'-D(*AP*AP*AP*GP*CP*CP*GP*CP*CP*C)-3')
E: PROTEIN (URACIL-DNA GLYCOSYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6974
Polymers31,5853
Non-polymers1121
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.830, 65.660, 97.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA chain DNA (5'-D(*TP*GP*GP*GP*(D1P)P*GP*GP*CP*TP*T)-3')


Mass: 2998.927 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*AP*AP*GP*CP*CP*GP*CP*CP*C)-3')


Mass: 2998.984 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (URACIL-DNA GLYCOSYLASE) / UDG / UNG


Mass: 25587.188 Da / Num. of mol.: 1 / Mutation: P82M, W83E, G84F, D145N, L272R
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
#4: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG40001reservoir
2100 mMHEPES1reservoir
31 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorDate: Apr 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 7140 / % possible obs: 97 % / Redundancy: 3.1 % / Rsym value: 0.108 / Net I/σ(I): 7.9
Reflection shellResolution: 2.9→3 Å / Rsym value: 0.398 / % possible all: 98
Reflection
*PLUS
Num. measured all: 21922 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.398

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Processing

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

1akz


Resolution: 2.9→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2.9
Details: THE ELECTRON DENSITY FOR THE DNA 5' OF THE URACIL-CONTAINING NUCLEOTIDE IS POOR. THE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATES REDUCED COB(II)ALAMIN (B12R), SINCE THERE IS NO ELECTRON ...Details: THE ELECTRON DENSITY FOR THE DNA 5' OF THE URACIL-CONTAINING NUCLEOTIDE IS POOR. THE COBALAMIN HAS BEEN MODELLED AS THE 5-COORDINATES REDUCED COB(II)ALAMIN (B12R), SINCE THERE IS NO ELECTRON DENSITY FOR AN ADENOSYL GROUP LINKED TO THE COBALT ATOM. HOWEVER, A HALF-OCCUPIED 5'-DEOXYADENOSINE HAS BEEN BUILT INTO ELECTRON DENSITY IN THE ACTIVE SITE (RESIDUES A803 AND AND C803). RESIDUES A801 AND A802 (AND C801, C802) REPRESENT AN EQUIMOLAR MIXTURE OF SUBSTRATE AND PRODUCT, SUCCINYL- AND METHYLMALONYL-COENZYME A.
RfactorNum. reflection% reflectionSelection details
Rfree0.273 711 10 %RANDOM
Rwork0.1891 ---
obs-6861 93.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-30.49 Å20 Å20 Å2
2--26.58 Å20 Å2
3---3.67 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 397 8 75 2291
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_deg1.392
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.66
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.391
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: 2.9→3.03 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.396 87 9.6 %
Rwork0.3566 6150 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM_NDBX.DNATOP_NDBX.DNA
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.66
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.391

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