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PDBsum entry 1pvu

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Type ii restriction endonuclease PDB id
1pvu
Jmol
Contents
Protein chains
154 a.a.
Waters ×79
PDB id:
1pvu
Name: Type ii restriction endonuclease
Title: The crystal structure of pvuii endonuclease reveals extensive structural homologies to ecorv
Structure: Pvu ii. Chain: a, b. Engineered: yes
Source: Proteus vulgaris. Organism_taxid: 585
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.184    
Authors: M.Vlassi,A.Athanasiadis
Key ref: A.Athanasiadis et al. (1994). Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV. Nat Struct Biol, 1, 469-475. PubMed id: 7664066
Date:
09-Mar-95     Release date:   31-Mar-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23657  (T2P2_PROHU) -  Type-2 restriction enzyme PvuII
Seq:
Struc:
157 a.a.
154 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  

 

 
Nat Struct Biol 1:469-475 (1994)
PubMed id: 7664066  
 
 
Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV.
A.Athanasiadis, M.Vlassi, D.Kotsifaki, P.A.Tucker, K.S.Wilson, M.Kokkinidis.
 
  ABSTRACT  
 
The crystal structure of the dimeric PvuII restriction endonuclease (R.PvuII) has been determined at a resolution of 2.4A. The protein has a mixed alpha/beta architecture and consists of two subdomains. Despite a lack of sequence homology, extensive structural similarities exist between one R.PvuII subdomain and the DNA-binding subdomain of EcoRV endonuclease (R.EcoRV); the dimerization subdomains are unrelated. Within the similar domains, flexible segments of R.PvuII are topologically equivalent to the DNA-binding turns of R.EcoRV; potential catalytic residues can be deduced from the structural similarities to R.EcoRV. Conformational flexibility is important for the interaction with DNA. A possible classification of endonuclease structures on the basis of the positions of the scissile phosphates is discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20587501 T.Raskó, A.Dér, E.Klement, K.Slaska-Kiss, E.Pósfai, K.F.Medzihradszky, D.R.Marshak, R.J.Roberts, and A.Kiss (2010).
BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism.
  Nucleic Acids Res, 38, 7155-7166.  
18456708 J.Orlowski, and J.M.Bujnicki (2008).
Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.
  Nucleic Acids Res, 36, 3552-3569.  
  17909283 C.Meramveliotaki, D.Kotsifaki, M.Androulaki, A.Hountas, E.Eliopoulos, and M.Kokkinidis (2007).
Purification, crystallization, X-ray diffraction analysis and phasing of an engineered single-chain PvuII restriction endonuclease.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 836-838.  
17369272 M.Y.Niv, D.R.Ripoll, J.A.Vila, A.Liwo, E.S.Vanamee, A.K.Aggarwal, H.Weinstein, and H.A.Scheraga (2007).
Topology of Type II REases revisited; structural classes and the common conserved core.
  Nucleic Acids Res, 35, 2227-2237.  
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.  
16195548 Q.S.Xu, R.J.Roberts, and H.C.Guo (2005).
Two crystal forms of the restriction enzyme MspI-DNA complex show the same novel structure.
  Protein Sci, 14, 2590-2600.
PDB code: 1yfi
15893669 S.A.Townson, J.C.Samuelson, S.Y.Xu, and A.K.Aggarwal (2005).
Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence.
  Structure, 13, 791-801.
PDB codes: 1vrr 1yuv
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.  
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.  
11742344 N.C.Horton, L.F.Dorner, and J.J.Perona (2002).
Sequence selectivity and degeneracy of a restriction endonuclease mediated by DNA intercalation.
  Nat Struct Biol, 9, 42-47.
PDB code: 1kc6
11842098 S.Grazulis, M.Deibert, R.Rimseliene, R.Skirgaila, G.Sasnauskas, A.Lagunavicius, V.Repin, C.Urbanke, R.Huber, and V.Siksnys (2002).
Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence.
  Nucleic Acids Res, 30, 876-885.
PDB code: 1knv
11557805 A.Pingoud, and A.Jeltsch (2001).
Structure and function of type II restriction endonucleases.
  Nucleic Acids Res, 29, 3705-3727.  
11179886 C.M.Lukacs, and A.K.Aggarwal (2001).
BglII and MunI: what a difference a base makes.
  Curr Opin Struct Biol, 11, 14-18.  
11331763 C.S.Bond, M.Kvaratskhelia, D.Richard, M.F.White, and W.N.Hunter (2001).
Structure of Hjc, a Holliday junction resolvase, from Sulfolobus solfataricus.
  Proc Natl Acad Sci U S A, 98, 5509-5514.
PDB code: 1hh1
11327870 S.L.Reid, D.Parry, H.H.Liu, and B.A.Connolly (2001).
Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization.
  Biochemistry, 40, 2484-2494.  
10911996 A.B.Hickman, Y.Li, S.V.Mathew, E.W.May, N.L.Craig, and F.Dyda (2000).
Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
  Mol Cell, 5, 1025-1034.
PDB code: 1f1z
10666447 E.A.Kubareva, H.Thole, A.S.Karyagina, T.S.Oretskaya, A.Pingoud, and V.Pingoud (2000).
Identification of a base-specific contact between the restriction endonuclease SsoII and its recognition sequence by photocross-linking.
  Nucleic Acids Res, 28, 1085-1091.  
10982859 L.Aravind, K.S.Makarova, and E.V.Koonin (2000).
SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories.
  Nucleic Acids Res, 28, 3417-3432.  
10648519 P.C.Hsieh, J.P.Xiao, D.O'loane, and S.Y.Xu (2000).
Cloning, expression, and purification of a thermostable nonhomodimeric restriction enzyme, BslI.
  J Bacteriol, 182, 949-955.  
10103058 C.M.Dupureur, and L.M.Hallman (1999).
Effects of divalent metal ions on the activity and conformation of native and 3-fluorotyrosine-PvuII endonucleases.
  Eur J Biochem, 261, 261-268.  
10508668 R.A.Kovall, and B.W.Matthews (1999).
Type II restriction endonucleases: structural, functional and evolutionary relationships.
  Curr Opin Chem Biol, 3, 578-583.  
10360178 S.E.Tsutakawa, T.Muto, T.Kawate, H.Jingami, N.Kunishima, M.Ariyoshi, D.Kohda, M.Nakagawa, and K.Morikawa (1999).
Crystallographic and functional studies of very short patch repair endonuclease.
  Mol Cell, 3, 621-628.
PDB code: 1vsr
9482749 C.Ban, and W.Yang (1998).
Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases.
  EMBO J, 17, 1526-1534.
PDB codes: 1azo 2azo
  9628339 F.Stahl, W.Wende, A.Jeltsch, and A.Pingoud (1998).
The mechanism of DNA cleavage by the type II restriction enzyme EcoRV: Asp36 is not directly involved in DNA cleavage but serves to couple indirect readout to catalysis.
  Biol Chem, 379, 467-473.  
9548954 F.Stahl, W.Wende, C.Wenz, A.Jeltsch, and A.Pingoud (1998).
Intra- vs intersubunit communication in the homodimeric restriction enzyme EcoRV: Thr 37 and Lys 38 involved in indirect readout are only important for the catalytic activity of their own subunit.
  Biochemistry, 37, 5682-5688.  
  9628337 J.R.Horton, J.Bonventre, and X.Cheng (1998).
How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?
  Biol Chem, 379, 451-458.
PDB code: 2pvi
  9628335 K.F.Lee, P.C.Shaw, S.J.Picone, G.G.Wilson, and K.D.Lunnen (1998).
Sequence comparison of the EcoHK31I and EaeI restriction-modification systems suggests an intergenic transfer of genetic material.
  Biol Chem, 379, 437-441.  
9736624 M.Newman, K.Lunnen, G.Wilson, J.Greci, I.Schildkraut, and S.E.Phillips (1998).
Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
  EMBO J, 17, 5466-5476.
PDB code: 1dmu
9653111 R.A.Kovall, and B.W.Matthews (1998).
Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases.
  Proc Natl Acad Sci U S A, 95, 7893-7897.  
9830053 W.Cao, and F.Barany (1998).
Identification of TaqI endonuclease active site residues by Fe2+-mediated oxidative cleavage.
  J Biol Chem, 273, 33002-33010.  
9287152 A.Lagunavicius, S.Grazulis, E.Balciunaite, D.Vainius, and V.Siksnys (1997).
DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: involvement of active site carboxylate residues.
  Biochemistry, 36, 11093-11099.  
9287151 A.Lagunavicius, and V.Siksnys (1997).
Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity.
  Biochemistry, 36, 11086-11092.  
9210460 A.Pingoud, and A.Jeltsch (1997).
Recognition and cleavage of DNA by type-II restriction endonucleases.
  Eur J Biochem, 246, 1.  
  9311818 A.Pujol, L.Deleu, J.P.Nüesch, C.Cziepluch, J.C.Jauniaux, and J.Rommelaere (1997).
Inhibition of parvovirus minute virus of mice replication by a peptide involved in the oligomerization of nonstructural protein NS1.
  J Virol, 71, 7393-7403.  
9298958 D.H.Groll, A.Jeltsch, U.Selent, and A.Pingoud (1997).
Does the restriction endonuclease EcoRV employ a two-metal-Ion mechanism for DNA cleavage?
  Biochemistry, 36, 11389-11401.  
9325303 H.G.Nastri, P.D.Evans, I.H.Walker, and P.D.Riggs (1997).
Catalytic and DNA binding properties of PvuII restriction endonuclease mutants.
  J Biol Chem, 272, 25761-25767.  
9254693 M.Belfort, and R.J.Roberts (1997).
Homing endonucleases: keeping the house in order.
  Nucleic Acids Res, 25, 3379-3388.  
9207015 W.Gong, M.O'Gara, R.M.Blumenthal, and X.Cheng (1997).
Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
  Nucleic Acids Res, 25, 2702-2715.
PDB code: 1boo
8919860 A.Jeltsch, and A.Pingoud (1996).
Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems.
  J Mol Evol, 42, 91-96.  
8917312 H.Ruan, K.D.Lunnen, M.E.Scott, L.S.Moran, B.E.Slatko, J.J.Pelletier, E.J.Hess, J.Benner, G.G.Wilson, and S.Y.Xu (1996).
Cloning and sequence comparison of AvaI and BsoBI restriction-modification systems.
  Mol Gen Genet, 252, 695-699.  
7739896 A.Chen, L.M.Powell, D.T.Dryden, N.E.Murray, and T.Brown (1995).
Tyrosine 27 of the specificity polypeptide of EcoKI can be UV crosslinked to a bromodeoxyuridine-substituted DNA target sequence.
  Nucleic Acids Res, 23, 1177-1183.  
7773740 A.K.Aggarwal (1995).
Structure and function of restriction endonucleases.
  Curr Opin Struct Biol, 5, 11-19.  
7896784 B.E.Withers, and J.C.Dunbar (1995).
Sequence-specific DNA recognition by the SmaI endonuclease.
  J Biol Chem, 270, 6496-6504.  
7724581 C.R.Robinson, and S.G.Sligar (1995).
Heterogeneity in molecular recognition by restriction endonucleases: osmotic and hydrostatic pressure effects on BamHI, Pvu II, and EcoRV specificity.
  Proc Natl Acad Sci U S A, 92, 3444-3448.  
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.