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- PDB-6vkp: Crystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dG -

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Basic information

Entry
Database: PDB / ID: 6vkp
TitleCrystal structure of DPO4 extension past 8-oxoadenine (oxoA) and dG
Components
  • DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*AP*GP*AP*TP*TP*CP*G)-3')
  • DNA (5'-D(*TP*TP*CP*AP*TP*(A38)P*GP*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*CP*C)-3')
  • DNA polymerase IV
KeywordsTRANSFERASE/DNA / DPO4 / Y-family DNA polymerase / Translesion synthesis / TRANSFERASE / extension / TRANSFERASE-DNA complex
Function / homology
Function and homology information


error-prone translesion synthesis / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / magnesium ion binding / cytoplasm
Similarity search - Function
DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain ...DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DZ4 / DNA / DNA (> 10) / DNA polymerase IV / DNA polymerase IV
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsJung, H. / Lee, S.
CitationJournal: Biochem.J. / Year: 2021
Title: Insights into the mismatch discrimination mechanism of Y-family DNA polymerase Dpo4.
Authors: Jung, H. / Lee, S.
History
DepositionJan 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 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
P: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*AP*GP*AP*TP*TP*CP*G)-3')
T: DNA (5'-D(*TP*TP*CP*AP*TP*(A38)P*GP*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*CP*C)-3')
A: DNA polymerase IV
B: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*AP*GP*AP*TP*TP*CP*G)-3')
C: DNA (5'-D(*TP*TP*CP*AP*TP*(A38)P*GP*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*CP*C)-3')
D: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,35012
Polymers98,2726
Non-polymers1,0786
Water1,17165
1
P: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*AP*GP*AP*TP*TP*CP*G)-3')
T: DNA (5'-D(*TP*TP*CP*AP*TP*(A38)P*GP*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*CP*C)-3')
A: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6756
Polymers49,1363
Non-polymers5393
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-48 kcal/mol
Surface area20490 Å2
MethodPISA
2
B: DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*AP*GP*AP*TP*TP*CP*G)-3')
C: DNA (5'-D(*TP*TP*CP*AP*TP*(A38)P*GP*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*CP*C)-3')
D: DNA polymerase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6756
Polymers49,1363
Non-polymers5393
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-48 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.098, 103.690, 99.105
Angle α, β, γ (deg.)90.000, 89.940, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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DNA chain , 2 types, 4 molecules PBTC

#1: DNA chain DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*AP*GP*AP*TP*TP*CP*G)-3')


Mass: 4409.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*TP*TP*CP*AP*TP*(A38)P*GP*AP*AP*TP*CP*TP*TP*TP*CP*CP*CP*CP*C)-3')


Mass: 5706.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 1 types, 2 molecules AD

#3: Protein DNA polymerase IV / Pol IV


Mass: 39019.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea)
Gene: dbh, SSOP1_2570, SULA_0242, SULB_0243, SULC_0242, SULG_01230, SULH_01230, SULI_01230, SULM_01230, SULN_01230, SULO_01240, SULZ_01250
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E3K6E9, UniProt: Q97W02*PLUS, DNA-directed DNA polymerase

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Non-polymers , 3 types, 71 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Tris 7.5 18% PEG 3350 100 mM magnesium acetate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.53→50 Å / Num. obs: 35565 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rpim(I) all: 0.064 / Net I/σ(I): 15.68
Reflection shellResolution: 2.53→2.57 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1729 / CC1/2: 0.478 / Rpim(I) all: 0.637

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JX4

1jx4


Resolution: 2.54→49.55 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2601 1855 5.22 %
Rwork0.2103 --
obs-35516 99.56 %
Displacement parametersBiso mean: 62.78 Å2
Refinement stepCycle: LAST / Resolution: 2.54→49.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 1308 64 65 6923
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01017088
X-RAY DIFFRACTIONf_angle_d1.23879808
X-RAY DIFFRACTIONf_chiral_restr0.09561120
X-RAY DIFFRACTIONf_plane_restr0.00621012
X-RAY DIFFRACTIONf_dihedral_angle_d25.36352922
LS refinement shellResolution: 2.54→2.6 Å
RfactorNum. reflection% reflection
Rfree0.3526 157 -
Rwork0.325 2432 -
obs--95 %

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