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- PDB-1nzp: Solution Structure of the Lyase Domain of Human DNA Polymerase Lambda -

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Basic information

Entry
Database: PDB / ID: 1nzp
TitleSolution Structure of the Lyase Domain of Human DNA Polymerase Lambda
ComponentsDNA polymerase lambda
KeywordsDNA BINDING PROTEIN/TRANSFERASE / DNA POLYMERASE LAMBDA / POL LAMBDA / LYASE DOMAIN / 8 kDa DOMAIN / POL BETA-LIKE / DNA BINDING PROTEIN-TRANSFERASE 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 / double-strand break repair via homologous recombination / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / 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 / double-strand break repair via homologous recombination / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / 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
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, 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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics follow by cartesian dynamics
Model type detailsminimized average
AuthorsDeRose, E.F. / Kirby, T.W. / Mueller, G.A. / Bebenek, K. / Garcia-Diaz, M. / Blanco, L. / Kunkel, T.A. / London, R.E.
CitationJournal: Biochemistry / Year: 2003
Title: Solution Structure of the Lyase Domain of Human DNA Polymerase Lambda
Authors: DeRose, E.F. / Kirby, T.W. / Mueller, G.A. / Bebenek, K. / Garcia-Diaz, M. / Blanco, L. / Kunkel, T.A. / London, R.E.
History
DepositionFeb 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase lambda


Theoretical massNumber of molelcules
Total (without water)9,7151
Polymers9,7151
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)8 / 20structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

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


Mass: 9715.243 Da / Num. of mol.: 1
Fragment: POLYMERASE LAMBDA LYASE DOMAIN(RESIDUES 242 - 327)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: Q9UGP5, DNA-directed DNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: Chemical shift assigments were made from 3D HNCACB, CBCA(CO)NH, HNCO, H(CCO)NH, and (H)C(CO)NH experiments. Aromatic resonances were assigned using 2D (HB)CB(CGCD)HD and (HB)CB(CGCDCE)HE experiments.

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Sample preparation

DetailsContents: 2mM pol lambda 8 kDa domain U-15N,13C; 5mM Tris-d11; 100mM NaCl; 1mM DTT; 5mM NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 5mM Tris, 100mM NaCl, 5mM NaN3 / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVarian, Inc.collection
NMRPipe2.1F. Delaglioprocessing
NMRView5.0.4B.A. Johnsondata analysis
CNS1A.T., Brunger et al.structure solution
ARIA1.1M. Nilgesstructure solution
ARIA1.1M. Nilgesrefinement
RefinementMethod: simulated annealing torsion angle dynamics follow by cartesian dynamics
Software ordinal: 1
Details: The structure was computed using default ARIA parameters. 281 manually assigned NOE distance restraints were used in addition to the NOE restraints automatically assigned by ARIA. ARIA ...Details: The structure was computed using default ARIA parameters. 281 manually assigned NOE distance restraints were used in addition to the NOE restraints automatically assigned by ARIA. ARIA assigned 790 unambiguous and 191 ambiguous NOE restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 8

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