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Hydrolase/DNA
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PDB id
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1pvi
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Enzyme class:
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E.C.3.1.21.4
- Type Ii site-specific deoxyribonuclease.
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Reaction:
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Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates.
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Cofactor:
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Magnesium
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Gene Ontology (GO) functional annotation
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Biological process
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DNA restriction-modification system
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1 term
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Biochemical function
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hydrolase activity
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5 terms
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Embo J
13:3927-3935
(1994)
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PubMed id:
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Structure of PvuII endonuclease with cognate DNA.
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X.Cheng,
K.Balendiran,
I.Schildkraut,
J.E.Anderson.
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ABSTRACT
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We have determined the structure of PvuII endonuclease complexed with cognate
DNA by X-ray crystallography. The DNA substrate is bound with a single
homodimeric protein, each subunit of which reveals three structural regions. The
catalytic region strongly resembles structures of other restriction
endonucleases, even though these regions have dissimilar primary sequences.
Comparison of the active site with those of EcoRV and EcoRI endonucleases
reveals a conserved triplet sequence close to the reactive phosphodiester group
and a conserved acidic pair that may represent the ligands for the catalytic
cofactor Mg2+. The DNA duplex is not significantly bent and maintains a
B-DNA-like conformation. The subunit interface region of the homodimeric protein
consists of a pseudo-three-helix bundle. Direct contacts between the protein and
the base pairs of the PvuII recognition site occur exclusively in the major
groove through two antiparallel beta strands from the sequence recognition
region of the protein. Water-mediated contacts are made in the minor grooves to
central bases of the site. If restriction enzymes do share a common ancestor, as
has been proposed, their catalytic regions have been very strongly conserved,
while their subunit interfaces and DNA sequence recognition regions have
undergone remarkable structural variation.
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Literature references that cite this PDB file's key reference
|
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| |
PubMed id
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|
Reference
|
|
|
|
|
|
M.Firczuk,
M.Wojciechowski,
H.Czapinska,
and
M.Bochtler
(2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
|
| |
Nucleic Acids Res, 39,
744-754.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
C.B.Prasannan,
F.Xie,
and
C.M.Dupureur
(2010).
Characterizing metalloendonuclease mixed metal complexes by global kinetic analysis.
|
| |
J Biol Inorg Chem, 15,
533-545.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
M.Sokolowska,
H.Czapinska,
and
M.Bochtler
(2009).
Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
|
| |
Nucleic Acids Res, 37,
3799-3810.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
R.D.Morgan,
and
Y.A.Luyten
(2009).
Rational engineering of type II restriction endonuclease DNA binding and cleavage specificity.
|
| |
Nucleic Acids Res, 37,
5222-5233.
|
|
|
|
|
|
|
N.Shaw,
W.Tempel,
J.Chang,
H.Yang,
C.Cheng,
J.Ng,
J.Rose,
Z.Rao,
B.C.Wang,
and
Z.J.Liu
(2008).
Crystal structure solution of a ParB-like nuclease at atomic resolution.
|
| |
Proteins, 70,
263-267.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
F.Reza,
P.Zuo,
and
J.Tian
(2007).
Protein interfacial pocket engineering via coupled computational filtering and biological focusing criterion.
|
| |
Ann Biomed Eng, 35,
1026-1036.
|
|
|
|
|
|
|
J.Kosinski,
E.Kubareva,
and
J.M.Bujnicki
(2007).
A model of restriction endonuclease MvaI in complex with DNA: a template for interpretation of experimental data and a guide for specificity engineering.
|
| |
Proteins, 68,
324-336.
|
|
|
|
|
|
|
G.Tamulaitiene,
A.Jakubauskas,
C.Urbanke,
R.Huber,
S.Grazulis,
and
V.Siksnys
(2006).
The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture.
|
| |
Structure, 14,
1389-1400.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Gu,
M.Gribskov,
and
P.E.Bourne
(2006).
Wiggle-predicting functionally flexible regions from primary sequence.
|
| |
PLoS Comput Biol, 2,
e90.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
D.J.Rigden
(2005).
An inactivated nuclease-like domain in RecC with novel function: implications for evolution.
|
| |
BMC Struct Biol, 5,
9.
|
|
|
|
|
|
|
E.S.Vanamee,
H.Viadiu,
R.Kucera,
L.Dorner,
S.Picone,
I.Schildkraut,
and
A.K.Aggarwal
(2005).
A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA.
|
| |
EMBO J, 24,
4198-4208.
|
|
|
PDB codes:
|
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|
|
H.Hashimoto,
T.Shimizu,
T.Imasaki,
M.Kato,
N.Shichijo,
K.Kita,
and
M.Sato
(2005).
Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA.
|
| |
J Biol Chem, 280,
5605-5610.
|
|
|
PDB codes:
|
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|
|
|
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|
|
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.
|
|
|
|
|
|
|
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:
|
|
|
|
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|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
M.Naderer,
J.R.Brust,
D.Knowle,
and
R.M.Blumenthal
(2002).
Mobility of a restriction-modification system revealed by its genetic contexts in three hosts.
|
| |
J Bacteriol, 184,
2411-2419.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
A.Pingoud,
and
A.Jeltsch
(2001).
Structure and function of type II restriction endonucleases.
|
| |
Nucleic Acids Res, 29,
3705-3727.
|
|
|
|
|
|
|
C.M.Dupureur,
and
M.A.Dominguez
(2001).
The PD...(D/E)XK motif in restriction enzymes: a link between function and conformation.
|
| |
Biochemistry, 40,
387-394.
|
|
|
|
|
|
|
C.M.Lukacs,
and
A.K.Aggarwal
(2001).
BglII and MunI: what a difference a base makes.
|
| |
Curr Opin Struct Biol, 11,
14-18.
|
|
|
|
|
|
|
M.A.Dominguez,
K.C.Thornton,
M.G.Melendez,
and
C.M.Dupureur
(2001).
Differential effects of isomeric incorporation of fluorophenylalanines into PvuII endonuclease.
|
| |
Proteins, 45,
55-61.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
S.R.Rajski,
and
J.K.Barton
(2001).
How different DNA-binding proteins affect long-range oxidative damage to DNA.
|
| |
Biochemistry, 40,
5556-5564.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
C.M.Dupureur,
and
L.H.Conlan
(2000).
A catalytically deficient active site variant of PvuII endonuclease binds Mg(II) ions.
|
| |
Biochemistry, 39,
10921-10927.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
M.R.Rice,
and
R.M.Blumenthal
(2000).
Recognition of native DNA methylation by the PvuII restriction endonuclease.
|
| |
Nucleic Acids Res, 28,
3143-3150.
|
|
|
|
|
|
|
N.M.Luscombe,
S.E.Austin,
H.M.Berman,
and
J.M.Thornton
(2000).
An overview of the structures of protein-DNA complexes.
|
| |
Genome Biol, 1,
REVIEWS001.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
Q.Huai,
J.D.Colandene,
Y.Chen,
F.Luo,
Y.Zhao,
M.D.Topal,
and
H.Ke
(2000).
Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase.
|
| |
EMBO J, 19,
3110-3118.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.D.Bruner,
D.P.Norman,
J.C.Fromme,
and
G.L.Verdine
(2000).
Structural and mechanistic studies on repair of 8-oxoguanine in mammalian cells.
|
| |
Cold Spring Harb Symp Quant Biol, 65,
103-111.
|
|
|
|
|
|
|
T.J.O'Loughlin,
Q.Xu,
R.B.Kucera,
L.F.Dorner,
S.Sweeney,
I.Schildkraut,
and
H.C.Guo
(2000).
Crystallization and preliminary X-ray diffraction analysis of MspI restriction endonuclease in complex with its cognate DNA.
|
| |
Acta Crystallogr D Biol Crystallogr, 56,
1652-1655.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
G.Malin,
R.Iakobashvili,
and
A.Lapidot
(1999).
Effect of tetrahydropyrimidine derivatives on protein-nucleic acids interaction. Type II restriction endonucleases as a model system.
|
| |
J Biol Chem, 274,
6920-6929.
|
|
|
|
|
|
|
K.Nadassy,
S.J.Wodak,
and
J.Janin
(1999).
Structural features of protein-nucleic acid recognition sites.
|
| |
Biochemistry, 38,
1999-2017.
|
|
|
|
|
|
|
R.A.Kovall,
and
B.W.Matthews
(1999).
Type II restriction endonucleases: structural, functional and evolutionary relationships.
|
| |
Curr Opin Chem Biol, 3,
578-583.
|
|
|
|
|
|
|
T.Dahai,
S.Ando,
Y.Takasaki,
and
J.Tadano
(1999).
Site-directed mutagenesis of restriction endonuclease HindIII.
|
| |
Biosci Biotechnol Biochem, 63,
1703-1707.
|
|
|
|
|
|
|
V.Tereshko,
and
J.A.Subirana
(1999).
Influence of packing interactions on the average conformation of B-DNA in crystalline structures.
|
| |
Acta Crystallogr D Biol Crystallogr, 55,
810-819.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
C.Wenz,
M.Hahn,
and
A.Pingoud
(1998).
Engineering of variants of the restriction endonuclease EcoRV that depend in their cleavage activity on the flexibility of sequences flanking the recognition site.
|
| |
Biochemistry, 37,
2234-2242.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
H.Viadiu,
and
A.K.Aggarwal
(1998).
The role of metals in catalysis by the restriction endonuclease BamHI.
|
| |
Nat Struct Biol, 5,
910-916.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.D.Colandene,
and
M.D.Topal
(1998).
The domain organization of NaeI endonuclease: separation of binding and catalysis.
|
| |
Proc Natl Acad Sci U S A, 95,
3531-3536.
|
|
|
|
|
|
|
M.Brickner,
and
J.Chmielewski
(1998).
Inhibiting the dimeric restriction endonuclease EcoRI using interfacial helical peptides.
|
| |
Chem Biol, 5,
339-343.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
N.C.Horton,
and
J.J.Perona
(1998).
Recognition of flanking DNA sequences by EcoRV endonuclease involves alternative patterns of water-mediated contacts.
|
| |
J Biol Chem, 273,
21721-21729.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
A.Pingoud,
and
A.Jeltsch
(1997).
Recognition and cleavage of DNA by type-II restriction endonucleases.
|
| |
Eur J Biochem, 246,
1.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
J.A.Subirana,
and
T.Faria
(1997).
Influence of sequence on the conformation of the B-DNA helix.
|
| |
Biophys J, 73,
333-338.
|
|
|
|
|
|
|
R.E.Dickerson,
and
T.K.Chiu
(1997).
Helix bending as a factor in protein/DNA recognition.
|
| |
Biopolymers, 44,
361-403.
|
|
|
|
|
|
|
R.Kovall,
and
B.W.Matthews
(1997).
Toroidal structure of lambda-exonuclease.
|
| |
Science, 277,
1824-1827.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.G.Erskine,
G.S.Baldwin,
and
S.E.Halford
(1997).
Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease.
|
| |
Biochemistry, 36,
7567-7576.
|
|
|
|
|
|
|
S.Windolph,
and
J.Alves
(1997).
Influence of divalent cations on inner-arm mutants of restriction endonuclease EcoRI.
|
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Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
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Nucleic Acids Res, 25,
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PDB code:
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X.Duan,
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Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity.
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Cell, 89,
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PDB code:
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Proc Natl Acad Sci U S A, 93,
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