Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje

Nucleic Acids Res. 2004 Oct 12;32(18):5442-51. doi: 10.1093/nar/gkh869. Print 2004.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / genetics
  • Archaeal Proteins / metabolism*
  • Base Sequence
  • Binding Sites
  • Catalysis
  • DNA, Cruciform / chemistry
  • DNA, Cruciform / metabolism*
  • Evolution, Molecular
  • Holliday Junction Resolvases / chemistry*
  • Holliday Junction Resolvases / genetics
  • Holliday Junction Resolvases / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Structure, Quaternary
  • Serine / chemistry
  • Substrate Specificity
  • Sulfates / metabolism
  • Sulfolobus / enzymology
  • Viral Proteins / genetics


  • Archaeal Proteins
  • DNA, Cruciform
  • Sulfates
  • Viral Proteins
  • Serine
  • Holliday Junction Resolvases

Associated data

  • PDB/1OB8
  • PDB/1OB9