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PDBsum entry 1eyu

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protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
1eyu
Jmol
Contents
Protein chains
156 a.a.
DNA/RNA
Waters ×366
PDB id:
1eyu
Name: Hydrolase/DNA
Title: High resolution structure of the pvuii endonculease/cognate DNA complex at ph 4.6
Structure: DNA (5'- d( Tp Gp Ap Cp Cp Ap Gp Cp Tp Gp Gp Tp C)-3'). Chain: c, d. Engineered: yes. Other_details: self-annealing oligonucleotide containing cognate six base pair sequence. Type ii restriction enzyme pvuii. Chain: a, b. Synonym: pvuii endonuclease, r.Pvuii.
Source: Synthetic: yes. Proteus vulgaris. Organism_taxid: 585. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.78Å     R-factor:   0.208     R-free:   0.243
Authors: J.R.Horton,X.Cheng
Key ref:
J.R.Horton and X.Cheng (2000). PvuII endonuclease contains two calcium ions in active sites. J Mol Biol, 300, 1049-1056. PubMed id: 10903853 DOI: 10.1006/jmbi.2000.3938
Date:
09-May-00     Release date:   21-Jul-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23657  (T2P2_PROHU) -  Type-2 restriction enzyme PvuII
Seq:
Struc:
157 a.a.
156 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.21.4  - Type Ii site-specific deoxyribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
      Cofactor: Mg(2+)
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleic acid phosphodiester bond hydrolysis   3 terms 
  Biochemical function     hydrolase activity     5 terms  

 

 
DOI no: 10.1006/jmbi.2000.3938 J Mol Biol 300:1049-1056 (2000)
PubMed id: 10903853  
 
 
PvuII endonuclease contains two calcium ions in active sites.
J.R.Horton, X.Cheng.
 
  ABSTRACT  
 
Restriction endonucleases differ in their use of metal cofactors despite having remarkably similar folds for their catalytic regions. To explore this, we have characterized the interaction of endonuclease PvuII with the catalytically incompetent cation Ca(2+). The structure of a glutaraldehyde-crosslinked crystal of the endonuclease PvuII-DNA complex, determined in the presence of Ca(2+) at a pH of approximately 6.5, supports a two-metal mechanism of DNA cleavage by PvuII. The first Ca(2+) position matches that found in all structurally examined endonucleases, while the second position is similar to that of EcoRV but is distinct from that of BamHI and BglI. The location of the second metal in PvuII, unlike that in BamHI/BglI, permits no direct interaction between the second metal and the O3' oxygen leaving group. However, the interactions between the DNA scissile phosphate and the metals, the first metal and the attacking water, and the attacking water and DNA are the same in PvuII as they are in the two-metal models of BamHI and BglI, but are distinct from the proposed three-metal or the two-metal models of EcoRV.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The primed active site of homodimeric PvuII-DNA complexes: (a) PvuII D34G mutant at pH 4.5 (pdb 3PVI; [Horton et al 1998b]), (b) PvuII at pH 4.5 in the presence of calcium (pdb 1EYU), and (c) crosslinked PvuII at pH 6.5 in the presence of calcium (pdb 1F0O). The calcium ions are labeled I and II and water molecules are labeled a, b, c in white lettering. Amino acid and nucleic acid residues are labeled with black lettering. The difference F[o] -F[c] electron density, contoured at 4.5s (green) and 8s (red) levels, illustrates the position of omitted water molecules and calcium ions. Arrows indicate the scissile bond.
Figure 2.
Figure 2. The octahedral coordination of two Ca^2+ observed in PvuII-DNA-Ca^2+ interactions. The numbers indicate the distance in Å between interacting atoms. Ca^2+ at site I has six coordination ligands including the attacking water (labeled a), and Ca^2+ at site II has five including the protonating water (labeled p), respectively.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 300, 1049-1056) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20703329 J.E.Deweese, and N.Osheroff (2010).
The Use of Divalent Metal Ions by Type II Topoisomerases.
  Metallomics, 2, 450-459.  
19161971 F.Xie, and C.M.Dupureur (2009).
Kinetic analysis of product release and metal ions in a metallonuclease.
  Arch Biochem Biophys, 483, 1-9.  
19815502 J.M.Wojciak, N.Zhu, K.T.Schuerenberg, K.Moreno, W.S.Shestowsky, M.Hiraiwa, R.Sabbadini, and T.Huxford (2009).
The crystal structure of sphingosine-1-phosphate in complex with a Fab fragment reveals metal bridging of an antibody and its antigen.
  Proc Natl Acad Sci U S A, 106, 17717-17722.
PDB code: 3i9g
18975919 F.Xie, S.H.Qureshi, G.A.Papadakos, and C.M.Dupureur (2008).
One- and two-metal ion catalysis: global single-turnover kinetic analysis of the PvuII endonuclease mechanism.
  Biochemistry, 47, 12540-12550.  
18653531 J.E.Deweese, A.B.Burgin, and N.Osheroff (2008).
Human topoisomerase IIalpha uses a two-metal-ion mechanism for DNA cleavage.
  Nucleic Acids Res, 36, 4883-4893.  
17308914 G.A.Papadakos, H.Nastri, P.Riggs, and C.M.Dupureur (2007).
Uncoupling metallonuclease metal ion binding sites via nudge mutagenesis.
  J Biol Inorg Chem, 12, 557-569.  
17214552 L.Mones, I.Simon, and M.Fuxreiter (2007).
Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism.
  Biol Chem, 388, 73-78.  
17557334 S.J.Kelly, J.Li, P.Setlow, and M.J.Jedrzejas (2007).
Structure, flexibility, and mechanism of the Bacillus stearothermophilus RecU Holliday junction resolvase.
  Proteins, 68, 961-971.
PDB code: 2fco
16710870 K.D.Roberts, J.N.Lambert, N.J.Ede, and A.M.Bray (2006).
Efficient methodology for the cyclization of linear peptide libraries via intramolecular S-alkylation using Multipin solid phase peptide synthesis.
  J Pept Sci, 12, 525-532.  
16600865 W.Yang, J.Y.Lee, and M.Nowotny (2006).
Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.
  Mol Cell, 22, 5.  
16209953 J.Y.Lee, J.Chang, N.Joseph, R.Ghirlando, D.N.Rao, and W.Yang (2005).
MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage.
  Mol Cell, 20, 155-166.
PDB codes: 2aoq 2aor
16356926 K.Eisenschmidt, T.Lanio, A.Simoncsits, A.Jeltsch, V.Pingoud, W.Wende, and A.Pingoud (2005).
Developing a programmed restriction endonuclease for highly specific DNA cleavage.
  Nucleic Acids Res, 33, 7039-7047.  
15684412 S.D.Pawlak, M.Radlinska, A.A.Chmiel, J.M.Bujnicki, and K.J.Skowronek (2005).
Inference of relationships in the 'twilight zone' of homology using a combination of bioinformatics and site-directed mutagenesis: a case study of restriction endonucleases Bsp6I and PvuII.
  Nucleic Acids Res, 33, 661-671.  
15805123 Z.Yang, J.R.Horton, R.Maunus, G.G.Wilson, R.J.Roberts, and X.Cheng (2005).
Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI.
  Nucleic Acids Res, 33, 1892-1901.
PDB code: 1ynm
15375161 S.Chandrashekaran, M.Saravanan, D.R.Radha, and V.Nagaraja (2004).
Ca(2+)-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease.
  J Biol Chem, 279, 49736-49740.  
14580211 L.M.Bowen, and C.M.Dupureur (2003).
Investigation of restriction enzyme cofactor requirements: a relationship between metal ion properties and sequence specificity.
  Biochemistry, 42, 12643-12653.  
12496295 T.Mordasini, A.Curioni, and W.Andreoni (2003).
Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of BamHI restriction endonuclease from combined quantum-classical simulations.
  J Biol Chem, 278, 4381-4384.  
12067333 A.S.Bhagwat, and M.Lieb (2002).
Cooperation and competition in mismatch repair: very short-patch repair and methyl-directed mismatch repair in Escherichia coli.
  Mol Microbiol, 44, 1421-1428.  
12237459 D.J.Rigden, P.Setlow, B.Setlow, I.Bagyan, R.A.Stein, and M.J.Jedrzejas (2002).
PrfA protein of Bacillus species: prediction and demonstration of endonuclease activity on DNA.
  Protein Sci, 11, 2370-2381.  
12142452 M.Fuxreiter, and I.Simon (2002).
Protein stability indicates divergent evolution of PD-(D/E)XK type II restriction endonucleases.
  Protein Sci, 11, 1978-1983.  
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
11250198 M.J.van der Woerd, J.J.Pelletier, S.Xu, and A.M.Friedman (2001).
Restriction enzyme BsoBI-DNA complex: a tunnel for recognition of degenerate DNA sequences and potential histidine catalysis.
  Structure, 9, 133-144.
PDB code: 1dc1
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.