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- PDB-1xsn: Crystal Structure of human DNA polymerase lambda in complex with ... -

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Basic information

Entry
Database: PDB / ID: 1xsn
TitleCrystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddTTP
Components
  • 5'-D(*CP*AP*GP*TP*AP*(2DT))-3'
  • 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'
  • 5'-D(P*GP*CP*CP*G)-3'
  • DNA polymerase lambda
KeywordsTRANSFERASE/DNA / DNA POLYMERASE LAMBDA / Protein-DNA complex / Helix-hairpin-helix / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA binding / nucleoplasm / metal ion binding / nucleus
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 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 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 (> 10) / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGarcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Kunkel, T.A. / Pedersen, L.C.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2005
Title: A closed conformation for the Pol lambda catalytic cycle.
Authors: Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Kunkel, T.A. / Pedersen, L.C.
#1: Journal: Mol.Cell / Year: 2004
Title: A Structural Solution for the DNA Polymerase-lambda Dependent Repair of DNA Gaps with Minimal Homology
Authors: Garcia-Diaz, M. / Bebenek, K. / Krahn, J.M. / Blanco, L. / Kunkel, T.A. / Pedersen, L.C.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: DNA polymerase lambda, a novel DNA repair enzyme in human cells
Authors: Garcia-Diaz, M. / Bebenek, K. / Sabariegos, R. / Dominguez, O. / Rodriguez, J. / Kirchhoff, T. / Garcia-Palomero, E. / Picher, A.J. / Juarez, R. / Ruiz, J.F. / Kunkel, T.A. / Blanco, L.
#3: Journal: J.Biol.Chem. / Year: 2003
Title: The frameshift Infidelity of human DNA polymerase lambda. Implications for function.
Authors: Bebenek, K. / Garcia-Diaz, K. / Blanco, L. / Kunkel, T.A.
#4: Journal: J.Biol.Chem. / Year: 2001
Title: Identification of an intrinsic 5'-deoxyribose-5-phosphate lyase activity in human DNA polymerase lambda: a possible role in Base Excision Repair
Authors: Garcia-Diaz, M. / Bebenek, K. / Kunkel, T.A. / Blanco, L.
History
DepositionOct 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'
P: 5'-D(*CP*AP*GP*TP*AP*(2DT))-3'
D: 5'-D(P*GP*CP*CP*G)-3'
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,57512
Polymers43,7904
Non-polymers7858
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.043, 62.551, 139.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe protein is a monomer thus the asymmetric unit represents the biological unit

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Components

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DNA chain , 3 types, 3 molecules TPD

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


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Template DNA
#2: DNA chain 5'-D(*CP*AP*GP*TP*AP*(2DT))-3'


Mass: 1792.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Primer DNA
#3: DNA chain 5'-D(P*GP*CP*CP*G)-3'


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Downstream Primer DNA

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Protein , 1 types, 1 molecules A

#4: Protein DNA polymerase lambda / Pol Lambda / DNA polymerase beta-2 / Pol beta2


Mass: 37447.688 Da / Num. of mol.: 1 / Fragment: 39 kDa catalytic C-terminal domain / Mutation: C543A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: pET22-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9UGP5, DNA-directed DNA polymerase

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Non-polymers , 5 types, 335 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-D3T / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE


Type: DNA OH 3 prime terminus / Mass: 466.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Sodium Citrate, 2-propanol, sodium chloride, cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Citrate11
22-propanol11
3sodium chloride11
4cacodylate11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.96318 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96318 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 34547 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 26.8 Å2 / Rsym value: 0.106 / Net I/σ(I): 15.7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.6 % / % possible all: 95.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 710728.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1632 4.9 %RANDOM
Rwork0.213 ---
all0.215 34659 --
obs0.213 33027 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.9222 Å2 / ksol: 0.378268 e/Å3
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1--5.4 Å20 Å20 Å2
2--4.98 Å20 Å2
3---0.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.95→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 425 47 327 3305
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.822
X-RAY DIFFRACTIONc_scangle_it4.042.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 253 5.1 %
Rwork0.264 4709 -
obs--83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4TER5APS.PARAMION.TOP
X-RAY DIFFRACTION5TER5APS.TOP

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