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- PDB-3uq2: Crystal structure of the post-catalytic product complex of polyme... -

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Basic information

Entry
Database: PDB / ID: 3uq2
TitleCrystal structure of the post-catalytic product complex of polymerase lambda with an rCMP inserted opposite a templating G and dAMP inserted opposite a templating T at the primer terminus.
Components
  • 5'-D(*CP*AP*GP*TP*AP)-R(P*CP*A)-3'
  • 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'
  • 5'-D(P*GP*CP*CP*G)-3'
  • DNA polymerase lambda
KeywordsTRANSFERASE / LYASE/DNA / DNA polymerase lambda / ribonucleotide incorporation / Protein Conformation / LYASE-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 replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / nucleus / metal ion binding
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 beta thumb / DNA polymerase, thumb domain superfamily / 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
PYROPHOSPHATE / DNA / DNA (> 10) / DNA/RNA hybrid / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 Å
AuthorsGosavi, R.A. / Moon, A.F. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda
Authors: Gosavi, R.A. / Moon, A.F. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K.
History
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Database references
Revision 1.2Sep 26, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_alt_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_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 lambda
T: 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'
P: 5'-D(*CP*AP*GP*TP*AP)-R(P*CP*A)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6097
Polymers43,3834
Non-polymers2253
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-59 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.286, 62.002, 141.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules TD

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


Mass: 3365.196 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain 5'-D(P*GP*CP*CP*G)-3'


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein / DNA/RNA hybrid , 2 types, 2 molecules AP

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


Mass: 36703.977 Da / Num. of mol.: 1 / Fragment: Loop mutant of DNA polymerase lambda / Mutation: SQEENGQQQ to KGET
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#3: DNA/RNA hybrid 5'-D(*CP*AP*GP*TP*AP)-R(P*CP*A)-3'


Mass: 2122.425 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 116 molecules

#5: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#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.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THIS IS A DELETION-SUBSTITUTION MUTANT, WITH RESIDUES SQEENGQQQ IN THE WILDTYPE ...AUTHORS STATE THAT THIS IS A DELETION-SUBSTITUTION MUTANT, WITH RESIDUES SQEENGQQQ IN THE WILDTYPE SUBSTITUTED BY RESIDUES KGET. HOWEVER, THE RESIDUE NUMBERING WAS KEPT CONSISTENT WITH THE WT PROTEIN.

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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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 170mM ammonium acetate, 85mM sodium citrate tribasic dihydrate pH 5.6, 25.5% (w/v) PEG4000, 15% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 24, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 23003 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 41.68 Å2 / Rsym value: 0.069 / Net I/σ(I): 23.7
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.288 / % possible all: 69.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_868)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3MGI

3mgi


Resolution: 2.25→27.13 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1089 4.86 %R free flags used from 3MGI
Rwork0.2111 ---
all0.2132 ---
obs0.213 22395 94.1 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.528 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--19.1779 Å2-0 Å20 Å2
2--30.1198 Å2-0 Å2
3----10.942 Å2
Refinement stepCycle: LAST / Resolution: 2.25→27.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 447 11 113 2966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072961
X-RAY DIFFRACTIONf_angle_d1.1994108
X-RAY DIFFRACTIONf_dihedral_angle_d13.448876
X-RAY DIFFRACTIONf_chiral_restr0.073459
X-RAY DIFFRACTIONf_plane_restr0.007451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.35240.3557990.25852108X-RAY DIFFRACTION76
2.3524-2.47630.32891220.24912362X-RAY DIFFRACTION85
2.4763-2.63130.35471320.24792630X-RAY DIFFRACTION94
2.6313-2.83430.27391490.24362774X-RAY DIFFRACTION99
2.8343-3.11920.29941470.24392797X-RAY DIFFRACTION100
3.1192-3.56970.26421370.21162801X-RAY DIFFRACTION99
3.5697-4.49410.22431500.18162843X-RAY DIFFRACTION100
4.4941-27.13190.21771530.2012991X-RAY DIFFRACTION99

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