1OB8

Holliday Junction Resolving Enzyme

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Substrate Recognition and Catalysis by the Holliday Junction Resolving Enzyme Hje.

Middleton, C.L., Parker, J.L., Richard, D.J., White, M.F., Bond, C.S.

(2004) Nucleic Acids Res 32: 5442

  • DOI: 10.1093/nar/gkh869
  • Primary Citation of Related Structures:  
    1OB9, 1OB8

  • PubMed Abstract: 

    • Two archaeal Holliday junction resolving enzymes, Holliday junction cleavage (Hjc) and Holliday junction endonuclease (Hje), have been characterized. Both are members of a nuclease superfamily that includes the type II restriction enzymes, although t ...

    Two archaeal Holliday junction resolving enzymes, Holliday junction cleavage (Hjc) and Holliday junction endonuclease (Hje), have been characterized. Both are members of a nuclease superfamily that includes the type II restriction enzymes, although their DNA cleaving activity is highly specific for four-way junction structure and not nucleic acid sequence. Despite 28% sequence identity, Hje and Hjc cleave junctions with distinct cutting patterns--they cut different strands of a four-way junction, at different distances from the junction centre. We report the high-resolution crystal structure of Hje from Sulfolobus solfataricus. The structure provides a basis to explain the differences in substrate specificity of Hje and Hjc, which result from changes in dimer organization, and suggests a viral origin for the Hje gene. Structural and biochemical data support the modelling of an Hje:DNA junction complex, highlighting a flexible loop that interacts intimately with the junction centre. A highly conserved serine residue on this loop is shown to be essential for the enzyme's activity, suggesting a novel variation of the nuclease active site. The loop may act as a conformational switch, ensuring that the active site is completed only on binding a four-way junction, thus explaining the exquisite specificity of these enzymes.

    Organizational Affiliation: 

    Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HOLLIDAY-JUNCTION RESOLVASEA, B135Saccharolobus solfataricusMutation(s): 0 
EC: 3.1.22.4
Find proteins for Q97YX6 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore Q97YX6 
Go to UniProtKB:  Q97YX6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
EDO
Query on EDO
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A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.577α = 90
b = 90.577β = 90
c = 70.92γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Source and taxonomy
  • Version 1.5: 2019-03-06
    Changes: Data collection, Experimental preparation