5F4H

Archael RuvB-like Holiday junction helicase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and Function of a Novel ATPase that Interacts with Holliday Junction Resolvase Hjc and Promotes Branch Migration.

Zhai, B.DuPrez, K.Doukov, T.I.Li, H.Huang, M.Shang, G.Ni, J.Gu, L.Shen, Y.Fan, L.

(2017) J Mol Biol 429: 1009-1029

  • DOI: 10.1016/j.jmb.2017.02.016
  • Primary Citation of Related Structures:  
    5F4H

  • PubMed Abstract: 
  • Holliday junction (HJ) is a hallmark intermediate in DNA recombination and must be processed by dissolution (for double HJ) or resolution to ensure genome stability. Although HJ resolvases have been identified in all domains of life, there is a long-standing effort to search in prokaryotes and eukarya for proteins promoting HJ migration ...

    Holliday junction (HJ) is a hallmark intermediate in DNA recombination and must be processed by dissolution (for double HJ) or resolution to ensure genome stability. Although HJ resolvases have been identified in all domains of life, there is a long-standing effort to search in prokaryotes and eukarya for proteins promoting HJ migration. Here, we report the structural and functional characterization of a novel ATPase, Sulfolobus islandicusPilT N-terminal-domain-containing ATPase (SisPINA), encoded by the gene adjacent to the resolvase Hjc coding gene. PINA is conserved in archaea and vital for S. islandicus viability. Purified SisPINA forms hexameric rings in the crystalline state and in solution, similar to the HJ migration helicase RuvB in Gram-negative bacteria. Structural analysis suggests that ATP binding and hydrolysis cause conformational changes in SisPINA to drive branch migration. Further studies reveal that SisPINA interacts with SisHjc and coordinates HJ migration and cleavage.


    Organizational Affiliation

    Department of Biochemistry, University of California, Riverside, CA 92521, USA. Electronic address: lifan@ucr.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nucleotide binding protein PINcA, B, C, D, E, F505Sulfolobus islandicus L.S.2.15Mutation(s): 1 
Gene Names: LS215_1665
UniProt
Find proteins for C3MQK6 (Sulfolobus islandicus (strain L.S.2.15 / Lassen #1))
Explore C3MQK6 
Go to UniProtKB:  C3MQK6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth E] , CA [auth E] , DA [auth E] , EA [auth E] , FA [auth E] , G [auth A] , GA [auth F] , H [auth A] , 
BA [auth E],  CA [auth E],  DA [auth E],  EA [auth E],  FA [auth E],  G [auth A],  GA [auth F],  H [auth A],  HA [auth F],  I [auth A],  IA [auth F],  JA [auth F],  L [auth B],  M [auth B],  R [auth C],  T [auth D],  U [auth D],  V [auth D],  W [auth D],  X [auth D],  Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D] , J [auth A] , K [auth A] , KA [auth F] , LA [auth F] , N [auth B] , O [auth B] , P [auth B] , 
AA [auth D],  J [auth A],  K [auth A],  KA [auth F],  LA [auth F],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  S [auth C],  Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.72α = 90
b = 148.98β = 104.07
c = 122.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
Blu-Icedata collection

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.2: 2017-11-01
    Changes: Database references