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PDBsum entry 1kcf
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Hydrolase PDB id
1kcf

 

 

 

 

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Contents
Protein chains
240 a.a. *
228 a.a. *
Ligands
SO4 ×2
Waters ×220
* Residue conservation analysis
PDB id:
1kcf
Name: Hydrolase
Title: Crystal structure of the yeast mitochondrial holliday junction resolvase, ydc2
Structure: Hypothetical 30.2 kd protein c25g10.02 in chromosome i. Chain: a, b. Engineered: yes
Source: Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Gene: spac25g10.02. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.30Å     R-factor:   0.238     R-free:   0.270
Authors: S.Ceschini,A.Keeley,M.S.B.Mcalister,M.Oram,J.Phelan,L.H.Pearl, I.R.Tsaneva,T.E.Barrett
Key ref:
S.Ceschini et al. (2001). Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2. EMBO J, 20, 6601-6611. PubMed id: 11726496 DOI: 10.1093/emboj/20.23.6601
Date:
08-Nov-01     Release date:   28-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q10423  (CCE1_SCHPO) -  Cruciform cutting endonuclease 1, mitochondrial from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Seq:
Struc: 		258 a.a.
240 a.a.
Protein chain
Pfam   ArchSchema ?
Q10423  (CCE1_SCHPO) -  Cruciform cutting endonuclease 1, mitochondrial from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Seq:
Struc: 		258 a.a.
228 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.3.1.21.10  - crossover junction endodeoxyribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1093/emboj/20.23.6601 EMBO J 20:6601-6611 (2001)
PubMed id: 11726496  
 
 
Crystal structure of the fission yeast mitochondrial Holliday junction resolvase Ydc2.
S.Ceschini, A.Keeley, M.S.McAlister, M.Oram, J.Phelan, L.H.Pearl, I.R.Tsaneva, T.E.Barrett.
 
  ABSTRACT  
 
Resolution of Holliday junctions into separate DNA duplexes requires enzymatic cleavage of an equivalent strand from each contributing duplex at or close to the point of strand exchange. Diverse Holliday junction-resolving enzymes have been identified in bacteria, bacteriophages, archaea and pox viruses, but the only eukaryotic examples identified so far are those from fungal mitochondria. We have now determined the crystal structure of Ydc2 (also known as SpCce1), a Holliday junction resolvase from the fission yeast Schizosaccharomyces pombe that is involved in the maintenance of mitochondrial DNA. This first structure of a eukaryotic Holliday junction resolvase confirms a distant evolutionary relationship to the bacterial RuvC family, but reveals structural features which are unique to the eukaryotic enzymes. Detailed analysis of the dimeric structure suggests mechanisms for junction isomerization and communication between the two active sites, and together with site-directed mutagenesis identifies residues involved in catalysis.
 
  Selected figure(s)  
 
Figure 5.
Figure 5 Active site variability and communication. (A) Superposition of the active sites from the metal-ion bound monomer (yellow) and the metal-free monomer (green). Significant changes in conformation of side chains and in the order of adjacent segments of the polypeptide chain occur as a result of metal ion binding. (B) A pathway for communication between the two active sites is provided by the direct interaction of the N-termini of helix 4 at the dimer interface. These are directly linked to the flexible 'pin' segments, which in turn connect to the active site metal ion ligand Glu117. Changes in the conformation of one active site would be communicated to the other site via this pathway, and could mediate the positive cooperativity observed between the first and second strand cleavage reactions. 		Figure 6.
Figure 6 Holliday junction complex. Model of a productive Ydc2 -Holliday junction complex. A model Holliday junction in an open, approximately square-planar conformation (transparent CPK model) can be docked onto the basic face of the Ydc2 dimer, bringing the scissile phosphodiester bonds close to the acidic cluster and the metal ion-binding site (red). The 'pin' and N-terminus of helix 4 that protrude from this face are accommodated by the centre of the open junction, but would prevent binding of the junction in a stacked-X conformation. Scissile phosphate groups are highlighted in yellow.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 6601-6611) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
20126554 C.D.Duncan, and K.M.Weeks (2010).
The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs.
  PLoS One, 5, e8983.  
20064926 E.M.Turk, and M.G.Caprara (2010).
Splicing of yeast aI5beta group I intron requires SUV3 to recycle MRS1 via mitochondrial degradosome-promoted decay of excised intron ribonucleoprotein (RNP).
  J Biol Chem, 285, 8585-8594.  
20203129 J.M.Svendsen, and J.W.Harper (2010).
GEN1/Yen1 and the SLX4 complex: Solutions to the problem of Holliday junction resolution.
  Genes Dev, 24, 521-536.  
19136958 B.Dalhus, A.S.Arvai, I.Rosnes, ..E.Olsen, P.H.Backe, I.Alseth, H.Gao, W.Cao, J.A.Tainer, and M.Bjørås (2009).
Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair.
  Nat Struct Mol Biol, 16, 138-143.
PDB codes: 2w35 2w36
19399178 F.Osman, L.Gaskell, and M.C.Whitby (2009).
Efficient second strand cleavage during holliday junction resolution by RuvC requires both increased junction flexibility and an exposed 5' phosphate.
  PLoS ONE, 4, e5347.  
19165139 M.Nowotny (2009).
Retroviral integrase superfamily: the structural perspective.
  EMBO Rep, 10, 144-151.  
18831036 R.Suzuki, H.Shindo, A.Tase, Y.Kikuchi, M.Shimizu, and T.Yamazaki (2009).
Solution structures and DNA binding properties of the N-terminal SAP domains of SUMO E3 ligases from Saccharomyces cerevisiae and Oryza sativa.
  Proteins, 75, 336-347.
PDB codes: 2rnn 2rno
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.  
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
17245438 E.Karakas, J.J.Truglio, D.Croteau, B.Rhau, L.Wang, B.Van Houten, and C.Kisker (2007).
Structure of the C-terminal half of UvrC reveals an RNase H endonuclease domain with an Argonaute-like catalytic triad.
  EMBO J, 26, 613-622.
PDB codes: 2nrr 2nrt 2nrv 2nrw 2nrx 2nrz
17890227 M.J.Culyba, N.Minkah, Y.Hwang, O.M.Benhamou, and F.D.Bushman (2007).
DNA branch nuclease activity of vaccinia A22 resolvase.
  J Biol Chem, 282, 34644-34652.  
16630276 J.Nosek, L.Tomaska, M.Bolotin-Fukuhara, and I.Miyakawa (2006).
Mitochondrial chromosome structure: an insight from analysis of complete yeast genomes.
  FEMS Yeast Res, 6, 356-370.  
17028102 R.Macmaster, S.Sedelnikova, P.J.Baker, E.L.Bolt, R.G.Lloyd, and J.B.Rafferty (2006).
RusA Holliday junction resolvase: DNA complex structure--insights into selectivity and specificity.
  Nucleic Acids Res, 34, 5577-5584.
PDB codes: 2h8c 2h8e
15720544 F.A.Curtis, P.Reed, and G.J.Sharples (2005).
Evolution of a phage RuvC endonuclease for resolution of both Holliday and branched DNA junctions.
  Mol Microbiol, 55, 1332-1345.  
15989951 M.Nowotny, S.A.Gaidamakov, R.J.Crouch, and W.Yang (2005).
Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.
  Cell, 121, 1005-1016.
PDB codes: 1zbf 1zbi 1zbl
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
16165328 ..Knizewski, and K.Ginalski (2005).
Bacillus subtilis YkuK protein is distantly related to RNase H.
  FEMS Microbiol Lett, 251, 341-346.  
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
15133049 S.Okubo, F.Hara, Y.Tsuchida, S.Shimotakahara, S.Suzuki, H.Hatanaka, S.Yokoyama, H.Tanaka, H.Yasuda, and H.Shindo (2004).
NMR structure of the N-terminal domain of SUMO ligase PIAS1 and its interaction with tumor suppressor p53 and A/T-rich DNA oligomers.
  J Biol Chem, 279, 31455-31461.
PDB code: 1v66
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.  
12823554 B.Sigala, and I.R.Tsaneva (2003).
Functional dissection of the Schizosaccharomyces pombe Holliday junction resolvase Ydc2: in vivo role in mitochondrial DNA maintenance.
  Eur J Biochem, 270, 2837-2847.  
12748193 J.S.Ahn, and M.C.Whitby (2003).
The role of the SAP motif in promoting Holliday junction binding and resolution by SpCCE1.
  J Biol Chem, 278, 29121-29129.  
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.  
11856858 J.H.Thorpe, S.C.Teixeira, B.C.Gale, and C.J.Cardin (2002).
Structural characterization of a new crystal form of the four-way Holliday junction formed by the DNA sequence d(CCGGTACCGG)2: sequence versus lattice?
  Acta Crystallogr D Biol Crystallogr, 58, 567-569.
PDB code: 1juc
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 codes are shown on the right.

 

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