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- PDB-4nm2: Structure of human DNA polymerase beta complexed with a nicked DN... -

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Basic information

Entry
Database: PDB / ID: 4nm2
TitleStructure of human DNA polymerase beta complexed with a nicked DNA containing a 8BrG-G at N-1 position and G-C at N position
Components
  • 5'-D(*CP*CP*GP*AP*CP*GP*(BGM)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'
  • 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*GP*C)-3'
  • 5'-D(P*GP*TP*CP*GP*G)-3'
  • DNA polymerase beta
KeywordsTRANSFERASE / LYASE/DNA / DNA binding / helix-turn-helix motif / polymerase fold / nucleotidyl transferase / nucleus / LYASE-DNA complex
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / homeostasis of number of cells / POLB-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / PCNA-Dependent Long Patch Base Excision Repair / pyrimidine dimer repair / response to hyperoxia / somatic hypermutation of immunoglobulin genes / lymph node development / salivary gland morphogenesis / spleen development / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to gamma radiation / spindle microtubule / base-excision repair / DNA-templated DNA replication / double-strand break repair via nonhomologous end joining / intrinsic apoptotic signaling pathway in response to DNA damage / microtubule binding / in utero embryonic development / neuron apoptotic process / response to ethanol / microtubule / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / lyase activity / Ub-specific processing proteases / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / 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
DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.524 Å
AuthorsKoag, M.-C. / Min, K. / Monzingo, A.F. / Lee, S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural basis for promutagenicity of 8-halogenated Guanine.
Authors: Koag, M.C. / Min, K. / Lee, S.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Feb 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_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.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.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
A: DNA polymerase beta
T: 5'-D(*CP*CP*GP*AP*CP*GP*(BGM)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'
P: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*GP*C)-3'
D: 5'-D(P*GP*TP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4576
Polymers47,4114
Non-polymers462
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-43 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.731, 80.202, 55.109
Angle α, β, γ (deg.)90.00, 106.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta


Mass: 37536.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Production host: Escherichia coli (E. coli)
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 4948.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template
#3: DNA chain 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*GP*C)-3'


Mass: 3390.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: up primer
#4: DNA chain 5'-D(P*GP*TP*CP*GP*G)-3'


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: down primer

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Non-polymers , 2 types, 67 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.72 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 14-23% PEG3400, 350 mM sodium acetate, 50 mM imidazole, pH 7.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.524→52.812 Å / Num. all: 15453 / Num. obs: 14617 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellHighest resolution: 2.524 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.524→52.81 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.598 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 1.379 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27673 702 5 %RANDOM
Rwork0.20034 ---
obs0.20425 13337 90.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å2-0.55 Å2
2--0.94 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.524→52.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 655 2 65 3214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0183271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.8254548
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1345318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27923.966116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.93315445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1181517
X-RAY DIFFRACTIONr_chiral_restr0.1010.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212255
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.524→2.589 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.666 22 -
Rwork0.358 532 -
obs--49.73 %
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)
10.6586-0.0216-0.08510.26-0.01310.0138-0.00140.0161-0.0598-0.06430.0020.0363-0.001-0.0071-0.00060.0536-0.0024-0.00930.0973-0.00350.058311.598-2.01213.276
21.6369-0.10130.42630.8103-0.14170.12980.05930.190.224-0.0852-0.11060.04440.02150.06080.05140.07420.0021-0.00340.10240.03560.040721.03314.0129.63
31.3292-1.63151.11234.5266-0.16611.57620.14180.08040.147-0.4269-0.49260.3013-0.0288-0.02030.35080.0938-0.017-0.00320.2227-0.07510.137116.07916.76615.552
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 335
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2T1 - 16
4X-RAY DIFFRACTION3P1 - 11

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