7OM0 | pdb_00007om0

Structure of Primase-Helicase in SaPI5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7OM0

This is version 1.4 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7OLA

Literature

Staphylococcal self-loading helicases couple the staircase mechanism with inter domain high flexibility.

Qiao, C.Debiasi-Anders, G.Mir-Sanchis, I.

(2022) Nucleic Acids Res 50: 8349-8362

  • DOI: https://doi.org/10.1093/nar/gkac625
  • Primary Citation Related Structures: 
    7OLA, 7OM0, 7PDS

  • PubMed Abstract: 

    Replication is a crucial cellular process. Replicative helicases unwind DNA providing the template strand to the polymerase and promoting replication fork progression. Helicases are multi-domain proteins which use an ATPase domain to couple ATP hydrolysis with translocation, however the role that the other domains might have during translocation remains elusive. Here, we studied the unexplored self-loading helicases called Reps, present in Staphylococcus aureus pathogenicity islands (SaPIs). Our cryoEM structures of the PriRep5 from SaPI5 (3.3 Å), the Rep1 from SaPI1 (3.9 Å) and Rep1-DNA complex (3.1Å) showed that in both Reps, the C-terminal domain (CTD) undergoes two distinct movements respect the ATPase domain. We experimentally demonstrate both in vitro and in vivo that SaPI-encoded Reps need key amino acids involved in the staircase mechanism of translocation. Additionally, we demonstrate that the CTD's presence is necessary for the maintenance of full ATPase and helicase activities. We speculate that this high interdomain flexibility couples Rep's activities as initiators and as helicases.


  • Organizational Affiliation
    • Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.

Macromolecule Content 

  • Total Structure Weight: 561.08 kDa 
  • Atom Count: 22,042 
  • Modeled Residue Count: 2,657 
  • Deposited Residue Count: 4,782 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA primase797Staphylococcus aureusMutation(s): 0 
Gene Names: DQV53_04810EQ90_04155G6Y10_11370HMPREF2819_07670
UniProt
Find proteins for A0A1S5ZIL8 (Staphylococcus aureus)
Explore A0A1S5ZIL8 
Go to UniProtKB:  A0A1S5ZIL8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S5ZIL8
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.1-4122-000
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2022-08-24
    Changes: Database references
  • Version 1.3: 2024-07-10
    Changes: Data collection
  • Version 1.4: 2024-11-13
    Changes: Data collection, Structure summary