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- PDB-1k82: Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (... -

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Basic information

Entry
Database: PDB / ID: 1k82
TitleCrystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA
Components
  • 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
  • 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3'
  • formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE/DNA / PROTEIN-DNA COMPLEX / DNA REPAIR / BETA SANDWICH / ZINC FINGER / HELIX TWO-TURNS HELIX / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA-formamidopyrimidine glycosylase / base-excision repair, AP site formation / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair ...oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity / oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA-formamidopyrimidine glycosylase / base-excision repair, AP site formation / DNA N-glycosylase activity / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / endonuclease activity / damaged DNA binding / DNA damage response / zinc ion binding / metal ion binding
Similarity search - Function
Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins ...Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGilboa, R. / Zharkov, D.O. / Golan, G. / Fernandes, A.S. / Gerchman, S.E. / Matz, E. / Kycia, J.H. / Grollman, A.P. / Shoham, G.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA.
Authors: Gilboa, R. / Zharkov, D.O. / Golan, G. / Fernandes, A.S. / Gerchman, S.E. / Matz, E. / Kycia, J.H. / Grollman, A.P. / Shoham, G.
History
DepositionOct 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
E: 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3'
I: 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
F: 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3'
J: 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
G: 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3'
K: 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
H: 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3'
L: 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
A: formamidopyrimidine-DNA glycosylase
B: formamidopyrimidine-DNA glycosylase
C: formamidopyrimidine-DNA glycosylase
D: formamidopyrimidine-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,27016
Polymers152,00812
Non-polymers2624
Water8,989499
1
E: 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3'
I: 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
A: formamidopyrimidine-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0674
Polymers38,0023
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3'
J: 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
B: formamidopyrimidine-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0674
Polymers38,0023
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3'
K: 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
C: formamidopyrimidine-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0674
Polymers38,0023
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
H: 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3'
L: 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'
D: formamidopyrimidine-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0674
Polymers38,0023
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.704, 96.033, 96.228
Angle α, β, γ (deg.)90.00, 96.799, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3' / FAPY-DNA glycosylase / Fpg


Mass: 3934.546 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: DNA chain
5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3'


Mass: 3863.531 Da / Num. of mol.: 4 / Source method: obtained synthetically
#3: Protein
formamidopyrimidine-DNA glycosylase


Mass: 30203.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: fpg / Plasmid: pET-13a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: P05523, DNA-formamidopyrimidine glycosylase
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.22 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Ammonium Sulfate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2Ammonium Sulfate11
3cacodylate11
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mMTris-HCl1drop
25 mM1dropMgCl2
3460 mM1dropNaCl
51.8-2.0 mg/mlprotein1drop
630 %(w/v)PEG80001reservoir
70.2 Mammonium sulfate1reservoir
80.1 Msodium cacodylate1reservoirpH6.5

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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: Apr 29, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→34 Å / Num. all: 84396 / Num. obs: 84396 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.069 / Net I/σ(I): 11.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4 % / Num. unique all: 8405 / Rsym value: 0.265 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 34 Å / Num. measured all: 310926 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.265

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Processing

Software
NameVersionClassification
GLRFphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EE8 AND PDB ENTRY 1K3W

1ee8

1k3w


Resolution: 2.1→34 Å / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.265 4191 RANDOM
Rwork0.214 --
all-84374 -
obs-84374 -
Displacement parametersBiso mean: 37 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Num. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 2.1→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8149 2064 4 499 10716
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.02
X-RAY DIFFRACTIONc_bond_d0.1
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.99

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