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- PDB-3uxp: Co-crystal Structure of Rat DNA polymerase beta Mutator I260Q: En... -

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Basic information

Entry
Database: PDB / ID: 3uxp
TitleCo-crystal Structure of Rat DNA polymerase beta Mutator I260Q: Enzyme-DNA-ddTTP
Components
  • DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3'
  • DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3'
  • DNA polymerase beta
KeywordsTRANSFERASE / LYASE/DNA / pol beta / repair polymerase / BER / LYASE-DNA complex
Function / homology
Function and homology information


Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / PCNA-Dependent Long Patch Base Excision Repair / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / POLB-Dependent Long Patch Base Excision Repair / somatic diversification of immunoglobulins / Ub-specific processing proteases / immunoglobulin heavy chain V-D-J recombination / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / 5'-deoxyribose-5-phosphate lyase activity / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / base-excision repair, gap-filling / spleen development / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / spindle microtubule / response to gamma radiation / base-excision repair / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / neuron apoptotic process / response to ethanol / in utero embryonic development / microtubule / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / inflammatory response / DNA damage response / apoptotic process / enzyme binding / protein-containing complex / DNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain ...Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Beta Polymerase, domain 2 / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA polymerase beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.723 Å
AuthorsGridley, C.L. / Jaeger, J.
CitationJournal: Biochemistry / Year: 2013
Title: Structural Changes in the Hydrophobic Hinge Region Adversely Affect the Activity and Fidelity of the I260Q Mutator DNA Polymerase beta.
Authors: Gridley, C.L. / Rangarajan, S. / Firbank, S. / Dalal, S. / Sweasy, J.B. / Jaeger, J.
History
DepositionDec 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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
A: DNA polymerase beta
B: DNA polymerase beta
P: DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3'
T: DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3'
D: DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3'
E: DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,62315
Polymers86,5306
Non-polymers1,0939
Water73941
1
A: DNA polymerase beta
P: DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3'
T: DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8238
Polymers43,2653
Non-polymers5585
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-56 kcal/mol
Surface area18170 Å2
MethodPISA
2
B: DNA polymerase beta
D: DNA 5'-D(P*AP*TP*GP*TP*GP*AP*G)-3'
E: DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8007
Polymers43,2653
Non-polymers5354
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-51 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.321, 56.607, 93.144
Angle α, β, γ (deg.)90.00, 102.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase beta


Mass: 38403.734 Da / Num. of mol.: 2 / Mutation: I260Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Polb / Production host: Escherichia coli (E. coli)
References: UniProt: P06766, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 2 types, 4 molecules PDTE

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


Mass: 2177.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Primer DNA Strand
#3: DNA chain DNA 5'-D(P*AP*CP*TP*CP*AP*CP*AP*TP*A)-3'


Mass: 2683.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Template DNA Strand

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Non-polymers , 3 types, 50 molecules

#4: Chemical ChemComp-D3T / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE


Type: DNA OH 3 prime terminus / Mass: 466.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Peg3350, NaCl, Glycerol, Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2011
RadiationMonochromator: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. ...Monochromator: Monochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification. Mirror: Meridionally-bent fused silica mirror with palladium and uncoated stripes vertically-focusing at 6.6:1 demagnification.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.723→27.195 Å / Num. obs: 25030 / % possible obs: 90.08 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.7226-2.7907166
2.7907-2.866178
2.866-2.9503179
2.9503-3.0454182
3.0454-3.1541187
3.1541-3.2801191

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.723→27.195 Å / SU ML: 0.85 / σ(F): 0.09 / Phase error: 35.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2008 8.02 %random
Rwork0.2182 ---
all0.24 ---
obs0.2248 25030 90.08 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.015 Å2 / ksol: 0.271 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--10.8835 Å2-0 Å22.5565 Å2
2---13.1072 Å2-0 Å2
3---23.9908 Å2
Refinement stepCycle: LAST / Resolution: 2.723→27.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 624 63 41 5976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096136
X-RAY DIFFRACTIONf_angle_d1.4798402
X-RAY DIFFRACTIONf_dihedral_angle_d21.6932420
X-RAY DIFFRACTIONf_chiral_restr0.096912
X-RAY DIFFRACTIONf_plane_restr0.005982
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7226-2.79070.45491020.35141202X-RAY DIFFRACTION66
2.7907-2.8660.39931260.34881426X-RAY DIFFRACTION78
2.866-2.95030.43631420.32671403X-RAY DIFFRACTION79
2.9503-3.04540.37761250.31021466X-RAY DIFFRACTION82
3.0454-3.15410.37291380.2821563X-RAY DIFFRACTION87
3.1541-3.28010.3271380.26431673X-RAY DIFFRACTION91
3.2801-3.42920.34751460.26231655X-RAY DIFFRACTION92
3.4292-3.60960.38281440.25871747X-RAY DIFFRACTION95
3.6096-3.83510.32051600.22441753X-RAY DIFFRACTION97
3.8351-4.13030.2991510.18341763X-RAY DIFFRACTION96
4.1303-4.54420.24361560.16141815X-RAY DIFFRACTION99
4.5442-5.19780.24821570.17081824X-RAY DIFFRACTION98
5.1978-6.53370.28251550.20731817X-RAY DIFFRACTION99
6.5337-27.19590.25871680.19941915X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.31470.4113-0.09883.53110.3093.93750.29450.1087-0.17520.1357-0.12960.55450.846-0.2816-0.14160.5719-0.0692-0.0780.40890.03710.591-13.7385-11.4364-14.7591
22.6522-2.9223-0.76745.8095-0.19380.18170.0364-0.26020.08280.0993-0.1078-1.0255-0.06990.11780.10870.4917-0.0361-0.09220.5298-0.11210.916659.04213.5147-25.4678
36.13461.9349-2.44256.0563-1.86633.7915-0.14570.7499-0.6453-0.1342-0.1776-0.29420.2710.27950.2710.4091-0.0592-0.04170.5482-0.13270.49379.672-1.0881-24.7163
49.28872.2768-0.93945.80030.06022.9518-0.57930.89160.8937-0.62690.25140.5870.3458-0.68350.37120.5071-0.11220.03350.72090.04030.694335.469613.843-35.1046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:150 )A9 - 150
2X-RAY DIFFRACTION2( CHAIN B AND RESID 9:150 )B9 - 150
3X-RAY DIFFRACTION3( CHAIN A AND RESID 151:334 ) OR ( CHAIN P AND RESID 1:7 )A151 - 334
4X-RAY DIFFRACTION3( CHAIN A AND RESID 151:334 ) OR ( CHAIN P AND RESID 1:7 )P1 - 7
5X-RAY DIFFRACTION4( CHAIN B AND RESID 151:334 ) OR ( CHAIN D AND RESID 1:7 )B151 - 334
6X-RAY DIFFRACTION4( CHAIN B AND RESID 151:334 ) OR ( CHAIN D AND RESID 1:7 )D1 - 7

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