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- PDB-1kfv: Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA ... -

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Basic information

Entry
Database: PDB / ID: 1kfv
TitleCrystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.
Components
  • 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3'
  • 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3'
  • Formamido-pyrimidine DNA glycosylase
KeywordsHYDROLASE/DNA / DNA repair enzyme / Abasic site / DNA / N-glycosylase / AP lyase / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / damaged DNA binding / zinc 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. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / 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. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / 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 speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular replacement combined with MAD / Resolution: 2.55 Å
AuthorsSerre, L. / Pereira de Jesus, K. / Boiteux, S. / Zelwer, C. / Castaing, B.
CitationJournal: EMBO J. / Year: 2002
Title: Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.
Authors: Serre, L. / Pereira de Jesus, K. / Boiteux, S. / Zelwer, C. / Castaing, B.
History
DepositionNov 23, 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: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Refinement description
Category: database_2 / software ...database_2 / software / 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3'
E: 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3'
G: 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3'
H: 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3'
A: Formamido-pyrimidine DNA glycosylase
B: Formamido-pyrimidine DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,34310
Polymers78,0286
Non-polymers3154
Water97354
1
D: 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3'
E: 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3'
A: Formamido-pyrimidine DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1715
Polymers39,0143
Non-polymers1582
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3'
H: 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3'
B: Formamido-pyrimidine DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1715
Polymers39,0143
Non-polymers1582
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.880, 62.030, 80.970
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 4 molecules DGEH

#1: DNA chain 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3'


Mass: 3683.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: contains a 1,3 propanediol site (PDI)
#2: DNA chain 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3'


Mass: 4066.702 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#3: Protein Formamido-pyrimidine DNA glycosylase / FAPY-DNA glycosylase / FPG / MUTM


Mass: 31263.736 Da / Num. of mol.: 2 / Mutation: P1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: MUTM or FPG / Plasmid: pMAL-c / Production host: Escherichia coli (E. coli)
References: UniProt: P42371, DNA-formamidopyrimidine glycosylase

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Non-polymers , 3 types, 58 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: PEG4K, LiSO4, TCEP, Tris-HCl, spermidine, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG4K11
2LiSO411
3TCEP11
4Tris-HCl11
5spermidine11
Crystal grow
*PLUS
pH: 7.6 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES-NaOH1droppH7.6
2100 mM1dropNaCl
35 %glycerol1drop
41 mMTCEP1drop
50.1 mMPMSF1drop
66-10 mg/mlprotein1drop
70.2 M1reservoirLi2SO4
80.1 MTris-HCl1reservoirpH7.7
91 mMTCEP1reservoir
102 mMspermidine1reservoir
1128 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9788 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 20, 2001 / Details: mirrors
RadiationMonochromator: Si (111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.54→25 Å / Num. all: 22185 / Num. obs: 21897 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.053 / Net I/σ(I): 6.1
Reflection shellResolution: 2.54→2.67 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.209 / % possible all: 94.3
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Rmerge(I) obs: 0.288

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Processing

Software
NameVersionClassification
SnBphasing
SOLVEphasing
MOLREPphasing
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: Molecular replacement combined with MAD
Starting model: PDB ENTRY 1EE8

1ee8


Resolution: 2.55→25 Å / Isotropic thermal model: overall / Cross valid method: free R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: NCS restraints have been considered during refinement. THERE ARE TWO POSSIBLE POSITIONS FOR THE ZN ATOM IN MOLECULE B (SEE AZN and BZN).
RfactorNum. reflection% reflectionSelection details
Rfree0.285 2166 10 %random
Rwork0.251 ---
all-22062 --
obs-21858 99.1 %-
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 2.55→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4210 1026 14 54 5304
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
LS refinement shellResolution: 2.55→2.57 Å / Total num. of bins used: 43
RfactorNum. reflection% reflection
Rfree0.38 46 10 %
Rwork0.35 385 -
obs--78 %
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.285 / Rfactor Rwork: 0.251
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.38 / Rfactor Rwork: 0.35

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