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PDBsum entry 1hh1

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protein links
Holliday junction resolvase PDB id
1hh1
Jmol
Contents
Protein chain
125 a.a. *
Waters ×79
* Residue conservation analysis
PDB id:
1hh1
Name: Holliday junction resolvase
Title: The structure of hjc, a holliday junction resolving enzyme from sulfolobus solfataricus
Structure: Holliday junction resolving enzyme hjc. Chain: a. Engineered: yes
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.15Å     R-factor:   0.220     R-free:   0.281
Authors: C.S.Bond,M.Kvaratskhelia,D.Richard,M.F.White,W.N.Hunter
Key ref:
C.S.Bond et al. (2001). Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus. Proc Natl Acad Sci U S A, 98, 5509-5514. PubMed id: 11331763 DOI: 10.1073/pnas.091613398
Date:
18-Dec-00     Release date:   06-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7LXU0  (Q7LXU0_SULSO) -  Holliday junction resolvase Hjc
Seq:
Struc:
143 a.a.
125 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.22.4  - Crossover junction endodeoxyribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage at a junction such as a reciprocal single- stranded crossover between two homologous DNA duplexes (Holliday junction).
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   5 terms 
  Biochemical function     nucleic acid binding     7 terms  

 

 
DOI no: 10.1073/pnas.091613398 Proc Natl Acad Sci U S A 98:5509-5514 (2001)
PubMed id: 11331763  
 
 
Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus.
C.S.Bond, M.Kvaratskhelia, D.Richard, M.F.White, W.N.Hunter.
 
  ABSTRACT  
 
The 2.15-A structure of Hjc, a Holliday junction-resolving enzyme from the archaeon Sulfolobus solfataricus, reveals extensive structural homology with a superfamily of nucleases that includes type II restriction enzymes. Hjc is a dimer with a large DNA-binding surface consisting of numerous basic residues surrounding the metal-binding residues of the active sites. Residues critical for catalysis, identified on the basis of sequence comparisons and site-directed mutagenesis studies, are clustered to produce two active sites in the dimer, about 29 A apart, consistent with the requirement for the introduction of paired nicks in opposing strands of the four-way DNA junction substrate. Hjc displays similarity to the restriction endonucleases in the way its specific DNA-cutting pattern is determined but uses a different arrangement of nuclease subunits. Further structural similarity to a broad group of metal/phosphate-binding proteins, including conservation of active-site location, is observed. A high degree of conservation of surface electrostatic character is observed between Hjc and T4-phage endonuclease VII despite a complete lack of structural homology. A model of the Hjc-Holliday junction complex is proposed, based on the available functional and structural data.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. The DNA-binding surfaces of Hjc, T4 endonuclease VII, and RuvC colored by electrostatic potential (blue represents positive and red represents negative charge). For comparison, the surface of a Holliday junction (HJ) computer-modeled in the X-shaped global structure predicted for junction bound by Hjc also is shown. Prepared by using GRASP (41).
Figure 4.
Fig. 4. (a) A model of Holliday junction DNA bound to Hjc. Hjc is shown as Corey-Pauling-Koltun spheres with residues conserved among Hjc sequences (gray) and residues for which mutants are inactive (black). A green ball marks the proposed metal-binding site. DNA is shown as a phosphate-backbone trace (exchange strand, cyan; continuous strand, blue), with the cleavage point highlighted in red. Prepared by using MOLSCRIPT (36). (b) Varying arrangements of similar nuclease domains produce different DNA-nicking patterns for the resolving enzymes Hjc and RuvC and the endonucleases EcoRV and MunI. Gray shapes indicate nuclease domains, with black triangles at the nicking site. DNA is represented by hatched rectangles or a circle.
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21265740 M.F.White (2011).
Homologous recombination in the archaea: the means justify the ends.
  Biochem Soc Trans, 39, 15-19.  
20375162 S.K.Menon, B.J.Eilers, M.J.Young, and C.M.Lawrence (2010).
The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily.
  J Virol, 84, 5890-5897.
PDB code: 2w8m
19625490 N.T.Uyen, S.Y.Park, J.W.Choi, H.J.Lee, K.Nishi, and J.S.Kim (2009).
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.
  Nucleic Acids Res, 37, 6960-6969.
PDB code: 3h1t
18160275 A.C.Déclais, and D.M.Lilley (2008).
New insight into the recognition of branched DNA structure by junction-resolving enzymes.
  Curr Opin Struct Biol, 18, 86-95.  
18164032 A.Obarska-Kosinska, J.E.Taylor, P.Callow, J.Orlowski, J.M.Bujnicki, and G.G.Kneale (2008).
HsdR subunit of the type I restriction-modification enzyme EcoR124I: biophysical characterisation and structural modelling.
  J Mol Biol, 376, 438-452.  
  20098639 K.T.Ehmsen, and W.D.Heyer (2008).
Biochemistry of Meiotic Recombination: Formation, Processing, and Resolution of Recombination Intermediates.
  Genome Dyn Stab, 3, 91.  
17873859 C.Biertümpfel, W.Yang, and D.Suck (2007).
Crystal structure of T4 endonuclease VII resolving a Holliday junction.
  Nature, 449, 616-620.
PDB codes: 2qnc 2qnf
17623842 C.R.Guzzo, R.A.Nagem, J.A.Barbosa, and C.S.Farah (2007).
Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif.
  Proteins, 69, 644-651.
PDB code: 2g3w
17511810 D.T.Mackay, C.H.Botting, G.L.Taylor, and M.F.White (2007).
An acetylase with relaxed specificity catalyses protein N-terminal acetylation in Sulfolobus solfataricus.
  Mol Microbiol, 64, 1540-1548.  
17584917 L.Knizewski, L.N.Kinch, N.V.Grishin, L.Rychlewski, and K.Ginalski (2007).
Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
  BMC Struct Biol, 7, 40.  
17392342 R.Sukackaite, A.Lagunavicius, K.Stankevicius, C.Urbanke, C.Venclovas, and V.Siksnys (2007).
Restriction endonuclease BpuJI specific for the 5'-CCCGT sequence is related to the archaeal Holliday junction resolvase family.
  Nucleic Acids Res, 35, 2377-2389.  
  16511128 C.Biertümpfel, J.Basquin, R.P.Birkenbihl, D.Suck, and C.Sauter (2005).
Characterization of crystals of the Hjc resolvase from Archaeoglobus fulgidus grown in gel by counter-diffusion.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 684-687.  
15985153 D.J.Rigden (2005).
An inactivated nuclease-like domain in RecC with novel function: implications for evolution.
  BMC Struct Biol, 5, 9.  
  16511081 E.Ennifar, J.Basquin, R.Birkenbihl, and D.Suck (2005).
Purification, crystallization and preliminary X-ray diffraction studies of the archaeal virus resolvase SIRV2.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 507-509.  
16011798 J.Kosinski, M.Feder, and J.M.Bujnicki (2005).
The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function.
  BMC Bioinformatics, 6, 172.  
15720711 M.Feder, and J.M.Bujnicki (2005).
Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site.
  BMC Genomics, 6, 21.  
16154091 N.McGregor, S.Ayora, S.Sedelnikova, B.Carrasco, J.C.Alonso, P.Thaw, and J.Rafferty (2005).
The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence-specific cleavage.
  Structure, 13, 1341-1351.
PDB code: 1zp7
16084390 T.Nishino, K.Komori, Y.Ishino, and K.Morikawa (2005).
Structural and functional analyses of an archaeal XPF/Rad1/Mus81 nuclease: asymmetric DNA binding and cleavage mechanisms.
  Structure, 13, 1183-1192.
PDB code: 1x2i
15479781 C.L.Middleton, J.L.Parker, D.J.Richard, M.F.White, and C.S.Bond (2004).
Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje.
  Nucleic Acids Res, 32, 5442-5451.
PDB codes: 1ob8 1ob9
15570068 C.P.Guy, A.I.Majerník, J.P.Chong, and E.L.Bolt (2004).
A novel nuclease-ATPase (Nar71) from archaea is part of a proposed thermophilic DNA repair system.
  Nucleic Acids Res, 32, 6176-6186.  
15520813 Y.Liu, and S.C.West (2004).
Happy Hollidays: 40th anniversary of the Holliday junction.
  Nat Rev Mol Cell Biol, 5, 937-944.  
12628932 A.C.Déclais, J.M.Fogg, A.D.Freeman, F.Coste, J.M.Hadden, S.E.Phillips, and D.M.Lilley (2003).
The complex between a four-way DNA junction and T7 endonuclease I.
  EMBO J, 22, 1398-1409.  
14646089 T.A.Muranova, S.E.Sedelnikova, P.M.Leonard, A.Pasquo, E.L.Bolt, R.G.Lloyd, and J.B.Rafferty (2003).
Crystallization of RusA Holliday junction resolvase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 59, 2262-2264.  
11972790 G.J.Sharples, E.L.Bolt, and R.G.Lloyd (2002).
RusA proteins from the extreme thermophile Aquifex aeolicus and lactococcal phage r1t resolve Holliday junctions.
  Mol Microbiol, 44, 549-559.  
12093751 J.M.Hadden, A.C.Déclais, S.E.Phillips, and D.M.Lilley (2002).
Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.
  EMBO J, 21, 3505-3515.
PDB codes: 1m0d 1m0i
12144927 S.Cheley, L.Q.Gu, and H.Bayley (2002).
Stochastic sensing of nanomolar inositol 1,4,5-trisphosphate with an engineered pore.
  Chem Biol, 9, 829-838.  
11726496 S.Ceschini, A.Keeley, M.S.McAlister, M.Oram, J.Phelan, L.H.Pearl, I.R.Tsaneva, and T.E.Barrett (2001).
Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2.
  EMBO J, 20, 6601-6611.
PDB code: 1kcf
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.