5GHR

DNA replication protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication.

Oyama, T.Ishino, S.Shirai, T.Yamagami, T.Nagata, M.Ogino, H.Kusunoki, M.Ishino, Y.

(2016) Nucleic Acids Res 44: 9505-9517

  • DOI: https://doi.org/10.1093/nar/gkw789
  • Primary Citation of Related Structures:  
    5GHR, 5GHS, 5GHT

  • PubMed Abstract: 

    In eukaryotic DNA replication initiation, hexameric MCM (mini-chromosome maintenance) unwinds the template double-stranded DNA to form the replication fork. MCM is activated by two proteins, Cdc45 and GINS, which constitute the 'CMG' unwindosome complex together with the MCM core. The archaeal DNA replication system is quite similar to that of eukaryotes, but only limited knowledge about the DNA unwinding mechanism is available, from a structural point of view. Here, we describe the crystal structure of an archaeal GAN (GINS-associated nuclease) from Thermococcus kodakaraensis, the homolog of eukaryotic Cdc45, in both the free form and the complex with the C-terminal domain of the cognate Gins51 subunit (Gins51C). This first archaeal GAN structure exhibits a unique, 'hybrid' structure between the bacterial RecJ and the eukaryotic Cdc45. GAN possesses the conserved DHH and DHH1 domains responsible for the exonuclease activity, and an inserted CID (CMG interacting domain)-like domain structurally comparable to that in Cdc45, suggesting its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication. A structural comparison of the GAN-Gins51C complex with the GINS tetramer suggests that GINS uses the mobile Gins51C as a hook to bind GAN for CMG formation.


  • Organizational Affiliation

    Faculty of Life and Environmental Sciences, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan takujio@yamanashi.ac.jp.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SsDNA-specific exonuclease
A, C
477Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK1252
UniProt
Find proteins for Q5JGL0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JGL0 
Go to UniProtKB:  Q5JGL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JGL0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein
B, D
80Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: TK0536
UniProt
Find proteins for Q5JF31 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JF31 
Go to UniProtKB:  Q5JF31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JF31
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.097α = 90
b = 116.004β = 90
c = 234.597γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2016-10-12 
  • Deposition Author(s): Oyama, T.

Funding OrganizationLocationGrant Number
JSPSJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-10-09
    Changes: Data collection, Database references, Structure summary