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- PDB-6yi2: UvrD helicase RNA polymerase interactions are governed by UvrDs c... -

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Basic information

Entry
Database: PDB / ID: 6yi2
TitleUvrD helicase RNA polymerase interactions are governed by UvrDs carboxy terminal Tudor domain.
ComponentsDNA helicase
KeywordsPROTEIN BINDING / DNA-repair / Tudor / UvrD / TCR
Function / homology
Function and homology information


rolling circle DNA replication / single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / DNA helicase complex / nucleotide-excision repair, DNA duplex unwinding / DNA translocase activity / DNA 3'-5' helicase / recombinational repair / DNA duplex unwinding / single-stranded DNA helicase activity ...rolling circle DNA replication / single-stranded DNA-dependent ATP-dependent DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / DNA helicase complex / nucleotide-excision repair, DNA duplex unwinding / DNA translocase activity / DNA 3'-5' helicase / recombinational repair / DNA duplex unwinding / single-stranded DNA helicase activity / replication fork processing / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / SOS response / mismatch repair / DNA helicase activity / isomerase activity / nucleotide-excision repair / response to radiation / DNA helicase / hydrolase activity / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
DNA helicase, ATP-dependent, UvrD type / : / PcrA/UvrD tudor domain / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. ...DNA helicase, ATP-dependent, UvrD type / : / PcrA/UvrD tudor domain / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA helicase / DNA helicase II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
AuthorsKawale, A.A. / Burmann, B.B.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-04721 Sweden
Knut and Alice Wallenberg Foundation2016.0163 Sweden
CitationJournal: Commun Biol / Year: 2020
Title: UvrD helicase-RNA polymerase interactions are governed by UvrD's carboxy-terminal Tudor domain.
Authors: Kawale, A.A. / Burmann, B.M.
History
DepositionMar 31, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA helicase


Theoretical massNumber of molelcules
Total (without water)8,4531
Polymers8,4531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, monomer
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6360 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein DNA helicase


Mass: 8452.634 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: uvrD, ACU57_06555 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: A0A0P7NW33, UniProt: P03018*PLUS, DNA helicase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic22D 1H-13C HSQC aliphatic
131isotropic22D 1H-13C HSQC aromatic
141isotropic23D CBCA(CO)NH
151isotropic23D HN(CA)CB
161isotropic23D HNCA
171isotropic23D HNCO
191isotropic13D (H)CCH-TOCSY
181isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution / Contents: 650 uM [U-13C; U-15N] UvrD CTD, 90% H2O/10% D2O / Label: 13C15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 650 uM / Component: UvrD CTD / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 20 mM KPi, 50 mM KCl pH 6.5 / Ionic strength: 70 mM / Label: UvrD sample buffer / pH: 6.5 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
CYANA3.98.12Guntert, Mumenthaler and Wuthrichstructure calculation
Sparky1.413Goddardchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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