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- PDB-2jw5: Polymerase Lambda BRCT domain -

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Basic information

Entry
Database: PDB / ID: 2jw5
TitlePolymerase Lambda BRCT domain
ComponentsDNA polymerase lambda
KeywordsPROTEIN BINDING / BRCT domain / Family X Polymerase / nonhomologous end joining (NHEJ) / DNA damage / DNA repair / DNA replication / DNA synthesis / DNA-binding / DNA-directed DNA polymerase / Lyase / Manganese / Metal-binding / Nucleotidyltransferase / Nucleus / Phosphorylation / Polymorphism / Transferase
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 / metal ion binding / nucleus
Similarity search - Function
BRCT domain / DNA polymerase family X, beta-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 ...BRCT domain / DNA polymerase family X, beta-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 lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMueller, G.A. / Moon, A.F. / DeRose, E.F. / Pedersen, L.C. / London, R.E.
CitationJournal: To be Published
Title: Polymerase Lambda BRCT domain
Authors: Mueller, G.A. / Moon, A.F. / DeRose, E.F. / Davis, B.J. / Ramsden, D.A. / Pedersen, L.C. / London, R.E.
History
DepositionOct 5, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 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)11,6421
Polymers11,6421
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)12 / 24structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 11642.331 Da / Num. of mol.: 1 / Fragment: BRCT domain (residues 34-135)
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D HNHA
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11322D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
110 uM DSS, 25 mM TRIS, 75 mM sodium chloride, 1 mM [U-2H] DTT, 0.2 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
210 uM DSS, 25 mM TRIS, 75 mM sodium chloride, 1 mM [U-2H] DTT, 0.2 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 uMDSS1
25 mMTRIS1
75 mMsodium chloride1
1 mMDTT[U-2H]1
0.2 mMEDTA1
10 uMDSS2
25 mMTRIS2
75 mMsodium chloride2
1 mMDTT[U-2H]2
0.2 mMEDTA2
Sample conditionsIonic strength: 0.075 / pH: 7.5 / Pressure: ambient / Temperature: 283 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, F. et al.processing
NMRViewJohnson, B.A. et al.chemical shift assignment
NMRViewJohnson, B.A. et al.peak picking
VnmrJVariancollection
TALOSCornilescu, G. et al.data analysis
CYANAGuntert, P. et al.structure solution
X-PLOR NIHSchwieters, C.D. et al.refinement
ProcheckNMRLaskowski, R.A. et al.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Initial structures calculated with CYANA, no RDCs. Final 24 structures (12 submitted) calculated with XPLOR-NIH and RDC restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 24 / Conformers submitted total number: 12

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