5LKM | pdb_00005lkm

RadA bound to dTDP

PDB DOI: https://doi.org/10.2210/pdb5LKM/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2016-07-22 Released: 2017-06-07
Deposition Author(s): Rapisarda, C., Remaut, H., Fornzes, R.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.224 (Depositor), 0.229 (DCC)
R-Value Work:
0.183 (Depositor), 0.184 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Bacterial RadA is a DnaB-type helicase interacting with RecA to promote bidirectional D-loop extension.

Marie, L., Rapisarda, C., Morales, V., Berge, M., Perry, T., Soulet, A.L., Gruget, C., Remaut, H., Fronzes, R., Polard, P.

(2017) Nat Commun 8: 15638-15638

PubMed: 28561029 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/ncomms15638
Primary Citation Related Structures:
5LKM, 5LKQ

PubMed Abstract:
Homologous recombination (HR) is a central process of genome biology driven by a conserved recombinase, which catalyses the pairing of single-stranded DNA (ssDNA) with double-stranded DNA to generate a D-loop intermediate. Bacterial RadA is a conserved HR effector acting with RecA recombinase to promote ssDNA integration. The mechanism of this RadA-mediated assistance to RecA is unknown. Here, we report functional and structural analyses of RadA from the human pathogen Streptococcus pneumoniae. RadA is found to facilitate RecA-driven ssDNA recombination over long genomic distances during natural transformation. RadA is revealed as a hexameric DnaB-type helicase, which interacts with RecA to promote orientated unwinding of branched DNA molecules mimicking D-loop boundaries. These findings support a model of DNA branch migration in HR, relying on RecA-mediated loading of RadA hexamers on each strand of the recipient dsDNA in the D-loop, from which they migrate divergently to facilitate incorporation of invading ssDNA.

Organizational Affiliation

Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse F-31062, France.

Macromolecule Content

Total Structure Weight: 149.52 kDa
Atom Count: 8,608
Modeled Residue Count: 1,109
Deposited Residue Count: 1,356
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RadA	A, B, C	452	Streptococcus pneumoniae	Mutation(s): 0 Gene Names: radA, ERS022181_02072 EC: 3.6.4
UniProt
Find proteins for Q8DRP0 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DRP0 Go to UniProtKB: Q8DRP0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DRP0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TYD Query on TYD Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain H [auth C] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain H [auth C] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], H [auth C]	THYMIDINE-5'-DIPHOSPHATE C₁₀ H₁₆ N₂ O₁₁ P₂ UJLXYODCHAELLY-XLPZGREQSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain H [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.224 (Depositor), 0.229 (DCC)
R-Value Work: 0.183 (Depositor), 0.184 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.4	α = 90
b = 169.9	β = 90
c = 187.42	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
BUSTER	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHELXDE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-06-07

Deposition Author(s):

Rapisarda, C.

Remaut, H.

Fornzes, R.

Funding Organization	Location	Grant Number
European Research Council	France	--

Revision History (Full details and data files)

Version 1.0: 2017-06-07
Type: Initial release
Version 1.1: 2024-01-10
Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description, Structure summary