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Enzyme class:
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Chains A, B:
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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7 terms
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DOI no:
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Science
269:656-663
(1995)
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PubMed id:
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Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding.
|
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M.Newman,
T.Strzelecka,
L.F.Dorner,
I.Schildkraut,
A.K.Aggarwal.
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| |
ABSTRACT
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The crystal structure of restriction endonuclease Bam HI complexed to DNA has
been determined at 2.2 angstrom resolution. The DNA binds in the cleft and
retains a B-DNA type of conformation. The enzyme, however, undergoes a series of
conformational changes, including rotation of subunits and folding of disordered
regions. The most striking conformational change is the unraveling of
carboxyl-terminal alpha helices to form partially disordered "arms."
The arm from one subunit fits into the minor groove while the arm from the
symmetry related subunit follows the DNA sugar-phosphate backbone. Recognition
of DNA base pairs occurs primarily in the major groove, with a few interactions
occurring in the minor groove. Tightly bound water molecules play an equally
important role as side chain and main chain atoms in the recognition of base
pairs. The complex also provides new insights into the mechanism by which the
enzyme catalyzes the hydrolysis of DNA phosphodiester groups.
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Literature references that cite this PDB file's key reference
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| |
PubMed id
|
|
Reference
|
|
|
|
|
|
E.S.Vanamee,
H.Viadiu,
S.H.Chan,
A.Ummat,
A.M.Hartline,
S.Y.Xu,
and
A.K.Aggarwal
(2011).
Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI.
|
| |
Nucleic Acids Res, 39,
712-719.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
H.Hwang,
H.Kim,
and
S.Myong
(2011).
Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity.
|
| |
Proc Natl Acad Sci U S A, 108,
7414-7418.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
T.J.Petty,
S.Emamzadah,
L.Costantino,
I.Petkova,
E.S.Stavridi,
J.G.Saven,
E.Vauthey,
and
T.D.Halazonetis
(2011).
An induced fit mechanism regulates p53 DNA binding kinetics to confer sequence specificity.
|
| |
EMBO J, 30,
2167-2176.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.H.Too,
Z.Zhu,
S.H.Chan,
and
S.Y.Xu
(2010).
Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs.
|
| |
Nucleic Acids Res, 38,
1294-1303.
|
|
|
|
|
|
|
R.Rohs,
X.Jin,
S.M.West,
R.Joshi,
B.Honig,
and
R.S.Mann
(2010).
Origins of specificity in protein-DNA recognition.
|
| |
Annu Rev Biochem, 79,
233-269.
|
|
|
|
|
|
|
C.Chen,
K.Krause,
and
B.M.Pettitt
(2009).
Advantage of being a dimer for Serratia marcescens endonuclease.
|
| |
J Phys Chem B, 113,
511-521.
|
|
|
|
|
|
|
H.Kamberaj,
and
A.van der Vaart
(2009).
Correlated motions and interactions at the onset of the DNA-induced partial unfolding of Ets-1.
|
| |
Biophys J, 96,
1307-1317.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
S.M.Lippow,
P.M.Aha,
M.H.Parker,
W.J.Blake,
B.M.Baynes,
and
D.Lipovsek
(2009).
Creation of a type IIS restriction endonuclease with a long recognition sequence.
|
| |
Nucleic Acids Res, 37,
3061-3073.
|
|
|
|
|
|
|
Y.Yonetani,
and
H.Kono
(2009).
Sequence dependencies of DNA deformability and hydration in the minor groove.
|
| |
Biophys J, 97,
1138-1147.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
A.Pingoud,
and
W.Wende
(2007).
A sliding restriction enzyme pauses.
|
| |
Structure, 15,
391-393.
|
|
|
|
|
|
|
E.S.Vanamee,
J.Berriman,
and
A.K.Aggarwal
(2007).
An EM view of the FokI synaptic complex by single particle analysis.
|
| |
J Mol Biol, 370,
207-212.
|
|
|
|
|
|
|
S.A.Townson,
J.C.Samuelson,
Y.Bao,
S.Y.Xu,
and
A.K.Aggarwal
(2007).
BstYI bound to noncognate DNA reveals a "hemispecific" complex: implications for DNA scanning.
|
| |
Structure, 15,
449-459.
|
|
|
PDB code:
|
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|
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|
|
S.R.Bellamy,
S.E.Milsom,
Y.S.Kovacheva,
R.B.Sessions,
and
S.E.Halford
(2007).
A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease.
|
| |
J Mol Biol, 373,
1169-1183.
|
|
|
|
|
|
|
Y.T.Wang,
W.J.Yang,
C.L.Li,
L.G.Doudeva,
and
H.S.Yuan
(2007).
Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.
|
| |
Nucleic Acids Res, 35,
584-594.
|
|
|
PDB codes:
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|
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|
|
C.C.Bjorklund,
and
W.B.Davis
(2006).
Attenuation of DNA charge transport by compaction into a nucleosome core particle.
|
| |
Nucleic Acids Res, 34,
1836-1846.
|
|
|
|
|
|
|
C.Chen,
B.W.Beck,
K.Krause,
and
B.M.Pettitt
(2006).
Solvent participation in Serratia marcescens endonuclease complexes.
|
| |
Proteins, 62,
982-995.
|
|
|
|
|
|
|
G.J.Gemmen,
R.Millin,
and
D.E.Smith
(2006).
Tension-dependent DNA cleavage by restriction endonucleases: two-site enzymes are "switched off" at low force.
|
| |
Proc Natl Acad Sci U S A, 103,
11555-11560.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
A.Sarai,
and
H.Kono
(2005).
Protein-DNA recognition patterns and predictions.
|
| |
Annu Rev Biophys Biomol Struct, 34,
379-398.
|
|
|
|
|
|
|
B.van den Broek,
M.C.Noom,
and
G.J.Wuite
(2005).
DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway.
|
| |
Nucleic Acids Res, 33,
2676-2684.
|
|
|
|
|
|
|
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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|
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|
|
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:
|
|
|
|
|
|
|
|
M.Fuxreiter,
M.Mezei,
I.Simon,
and
R.Osman
(2005).
Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI.
|
| |
Biophys J, 89,
903-911.
|
|
|
|
|
|
|
N.Y.Sidorova,
S.Muradymov,
and
D.C.Rau
(2005).
Trapping DNA-protein binding reactions with neutral osmolytes for the analysis by gel mobility shift and self-cleavage assays.
|
| |
Nucleic Acids Res, 33,
5145-5155.
|
|
|
|
|
|
|
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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|
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|
|
R.A.O'Flanagan,
G.Paillard,
R.Lavery,
and
A.M.Sengupta
(2005).
Non-additivity in protein-DNA binding.
|
| |
Bioinformatics, 21,
2254-2263.
|
|
|
|
|
|
|
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:
|
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|
|
|
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|
|
S.Nikolajewa,
A.Beyer,
M.Friedel,
J.Hollunder,
and
T.Wilhelm
(2005).
Common patterns in type II restriction enzyme binding sites.
|
| |
Nucleic Acids Res, 33,
2726-2733.
|
|
|
|
|
|
|
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:
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|
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|
|
D.R.Edgell,
V.Derbyshire,
P.Van Roey,
S.LaBonne,
M.J.Stanger,
Z.Li,
T.M.Boyd,
D.A.Shub,
and
M.Belfort
(2004).
Intron-encoded homing endonuclease I-TevI also functions as a transcriptional autorepressor.
|
| |
Nat Struct Mol Biol, 11,
936-944.
|
|
|
PDB code:
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|
|
G.Fuentes,
A.Ballesteros,
and
C.S.Verma
(2004).
Specificity in lipases: a computational study of transesterification of sucrose.
|
| |
Protein Sci, 13,
3092-3103.
|
|
|
|
|
|
|
N.Y.Sidorova,
and
D.C.Rau
(2004).
Differences between EcoRI nonspecific and "star" sequence complexes revealed by osmotic stress.
|
| |
Biophys J, 87,
2564-2576.
|
|
|
|
|
|
|
A.Guasch,
M.Lucas,
G.Moncalián,
M.Cabezas,
R.Pérez-Luque,
F.X.Gomis-Rüth,
F.de la Cruz,
and
M.Coll
(2003).
Recognition and processing of the origin of transfer DNA by conjugative relaxase TrwC.
|
| |
Nat Struct Biol, 10,
1002-1010.
|
|
|
PDB codes:
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|
|
D.Liu,
W.T.Windsor,
and
D.F.Wyss
(2003).
Double-stranded DNA-induced localized unfolding of HCV NS3 helicase subdomain 2.
|
| |
Protein Sci, 12,
2757-2767.
|
|
|
|
|
|
|
I.Goldhaber-Gordon,
M.H.Early,
and
T.A.Baker
(2003).
MuA transposase separates DNA sequence recognition from catalysis.
|
| |
Biochemistry, 42,
14633-14642.
|
|
|
|
|
|
|
J.Sun,
H.Viadiu,
A.K.Aggarwal,
and
H.Weinstein
(2003).
Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex.
|
| |
Biophys J, 84,
3317-3325.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
N.Guhan,
and
K.Muniyappa
(2003).
Mycobacterium tuberculosis RecA intein, a LAGLIDADG homing endonuclease, displays Mn(2+) and DNA-dependent ATPase activity.
|
| |
Nucleic Acids Res, 31,
4184-4191.
|
|
|
|
|
|
|
E.P.van Someren,
L.F.Wessels,
E.Backer,
and
M.J.Reinders
(2002).
Genetic network modeling.
|
| |
Pharmacogenomics, 3,
507-525.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
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:
|
|
|
|
|
|
|
|
T.W.Lynch,
D.Kosztin,
M.A.McLean,
K.Schulten,
and
S.G.Sligar
(2002).
Dissecting the molecular origins of specific protein-nucleic acid recognition: hydrostatic pressure and molecular dynamics.
|
| |
Biophys J, 82,
93-98.
|
|
|
|
|
|
|
Z.Morávek,
S.Neidle,
and
B.Schneider
(2002).
Protein and drug interactions in the minor groove of DNA.
|
| |
Nucleic Acids Res, 30,
1182-1191.
|
|
|
|
|
|
|
A.Pingoud,
and
A.Jeltsch
(2001).
Structure and function of type II restriction endonucleases.
|
| |
Nucleic Acids Res, 29,
3705-3727.
|
|
|
|
|
|
|
C.M.Lukacs,
and
A.K.Aggarwal
(2001).
BglII and MunI: what a difference a base makes.
|
| |
Curr Opin Struct Biol, 11,
14-18.
|
|
|
|
|
|
|
H.Watrob,
W.Liu,
Y.Chen,
S.G.Bartlett,
L.Jen-Jacobson,
and
M.D.Barkley
(2001).
Solution conformation of EcoRI restriction endonuclease changes upon binding of cognate DNA and Mg2+ cofactor.
|
| |
Biochemistry, 40,
683-692.
|
|
|
|
|
|
|
L.S.Higgins,
C.Besnier,
and
H.Kong
(2001).
The nicking endonuclease N.BstNBI is closely related to type IIs restriction endonucleases MlyI and PleI.
|
| |
Nucleic Acids Res, 29,
2492-2501.
|
|
|
|
|
|
|
P.Romero,
Z.Obradovic,
X.Li,
E.C.Garner,
C.J.Brown,
and
A.K.Dunker
(2001).
Sequence complexity of disordered protein.
|
| |
Proteins, 42,
38-48.
|
|
|
|
|
|
|
S.A.Williams,
and
S.E.Halford
(2001).
SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site.
|
| |
Nucleic Acids Res, 29,
1476-1483.
|
|
|
|
|
|
|
S.Bergqvist,
R.O'Brien,
and
J.E.Ladbury
(2001).
Site-specific cation binding mediates TATA binding protein-DNA interaction from a hyperthermophilic archaeon.
|
| |
Biochemistry, 40,
2419-2425.
|
|
|
|
|
|
|
S.E.Tsutakawa,
and
K.Morikawa
(2001).
The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease.
|
| |
Nucleic Acids Res, 29,
3775-3783.
|
|
|
|
|
|
|
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.Millevoi,
L.Thion,
G.Joseph,
C.Vossen,
L.Ghisolfi-Nieto,
and
M.Erard
(2001).
Atypical binding of the neuronal POU protein N-Oct3 to noncanonical DNA targets. Implications for heterodimerization with HNF-3 beta.
|
| |
Eur J Biochem, 268,
781-791.
|
|
|
|
|
|
|
W.A.Breyer,
and
B.W.Matthews
(2001).
A structural basis for processivity.
|
| |
Protein Sci, 10,
1699-1711.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
H.Viadiu,
and
A.K.Aggarwal
(2000).
Structure of BamHI bound to nonspecific DNA: a model for DNA sliding.
|
| |
Mol Cell, 5,
889-895.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.J.Hlavaty,
J.S.Benner,
L.J.Hornstra,
and
I.Schildkraut
(2000).
Identification of the metal-binding sites of restriction endonucleases by Fe2+-mediated oxidative cleavage.
|
| |
Biochemistry, 39,
3097-3105.
|
|
|
|
|
|
|
K.B.Geahigan,
G.A.Meints,
M.E.Hatcher,
J.Orban,
and
G.P.Drobny
(2000).
The dynamic impact of CpG methylation in DNA.
|
| |
Biochemistry, 39,
4939-4946.
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
L.Jen-Jacobson,
L.E.Engler,
and
L.A.Jacobson
(2000).
Structural and thermodynamic strategies for site-specific DNA binding proteins.
|
| |
Structure, 8,
1015-1023.
|
|
|
|
|
|
|
N.M.Luscombe,
S.E.Austin,
H.M.Berman,
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PDB code:
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Cold Spring Harb Symp Quant Biol, 65,
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Identification of Asp218 and Asp326 as the principal Mg2+ binding ligands of the homing endonuclease PI-SceI.
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Biochemistry, 39,
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Acta Crystallogr D Biol Crystallogr, 56,
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Structural basis of multidrug recognition by BmrR, a transcription activator of a multidrug transporter.
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Cell, 96,
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PDB codes:
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F.H.Allain,
Y.M.Yen,
J.E.Masse,
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Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding.
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PDB code:
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J.Greenwald,
V.Le,
S.L.Butler,
F.D.Bushman,
and
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(1999).
The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity.
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Biochemistry, 38,
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PDB codes:
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M.Wolf-Watz,
X.Q.Xie,
M.Holm,
T.Grundström,
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Solution properties of the free and DNA-bound Runt domain of AML1.
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Eur J Biochem, 261,
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L.F.Dorner,
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(1999).
Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease-DNA complex.
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Acta Crystallogr D Biol Crystallogr, 55,
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S.E.Tsutakawa,
T.Muto,
T.Kawate,
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M.Ariyoshi,
D.Kohda,
M.Nakagawa,
and
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(1999).
Crystallographic and functional studies of very short patch repair endonuclease.
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Mol Cell, 3,
621-628.
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PDB code:
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S.J.Mannino,
C.L.Jenkins,
and
R.T.Raines
(1999).
Chemical mechanism of DNA cleavage by the homing endonuclease I-PpoI.
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Biochemistry, 38,
16178-16186.
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B.Ma,
C.J.Tsai,
H.Wolfson,
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(1999).
Folding funnels and conformational transitions via hinge-bending motions.
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Cell Biochem Biophys, 31,
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T.Brendler,
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Binding of SeqA protein to DNA requires interaction between two or more complexes bound to separate hemimethylated GATC sequences.
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EMBO J, 18,
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(1999).
Site-directed mutagenesis of restriction endonuclease HindIII.
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Biosci Biotechnol Biochem, 63,
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A.D.Frankel,
and
C.A.Smith
(1998).
Induced folding in RNA-protein recognition: more than a simple molecular handshake.
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Cell, 92,
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(1998).
Structural basis for MutH activation in E.coli mismatch repair and relationship of MutH to restriction endonucleases.
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EMBO J, 17,
1526-1534.
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PDB codes:
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|
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.
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Biochemistry, 37,
2234-2242.
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D.A.Wah,
J.Bitinaite,
I.Schildkraut,
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(1998).
Structure of FokI has implications for DNA cleavage.
|
| |
Proc Natl Acad Sci U S A, 95,
10564-10569.
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PDB code:
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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.
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Biol Chem, 379,
467-473.
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F.Stahl,
W.Wende,
C.Wenz,
A.Jeltsch,
and
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(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.
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Biochemistry, 37,
5682-5688.
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H.Viadiu,
and
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(1998).
The role of metals in catalysis by the restriction endonuclease BamHI.
|
| |
Nat Struct Biol, 5,
910-916.
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PDB codes:
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|
|
J.Bitinaite,
D.A.Wah,
A.K.Aggarwal,
and
I.Schildkraut
(1998).
FokI dimerization is required for DNA cleavage.
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Proc Natl Acad Sci U S A, 95,
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M.Gerstein,
and
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A database of macromolecular motions.
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Nucleic Acids Res, 26,
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M.Newman,
K.Lunnen,
G.Wilson,
J.Greci,
I.Schildkraut,
and
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(1998).
Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence.
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| |
EMBO J, 17,
5466-5476.
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PDB code:
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N.C.Horton,
K.J.Newberry,
and
J.J.Perona
(1998).
Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases.
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| |
Proc Natl Acad Sci U S A, 95,
13489-13494.
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PDB code:
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|
P.J.Pomposiello,
B.K.Janes,
and
R.A.Bender
(1998).
Two roles for the DNA recognition site of the Klebsiella aerogenes nitrogen assimilation control protein.
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J Bacteriol, 180,
578-585.
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W.Liu,
Y.Chen,
H.Watrob,
S.G.Bartlett,
L.Jen-Jacobson,
and
M.D.Barkley
(1998).
N-termini of EcoRI restriction endonuclease dimer are in close proximity on the protein surface.
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Biochemistry, 37,
15457-15465.
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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.
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Biochemistry, 36,
11086-11092.
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A.Pingoud,
and
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(1997).
Recognition and cleavage of DNA by type-II restriction endonucleases.
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| |
Eur J Biochem, 246,
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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?
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| |
Biochemistry, 36,
11389-11401.
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F.Conejero-Lara,
C.González,
M.A.Jiménez,
S.Padmanabhan,
P.L.Mateo,
and
M.Rico
(1997).
NMR solution structure of the 205-316 C-terminal fragment of thermolysin. An example of dimerization coupled to partial unfolding.
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| |
Biochemistry, 36,
11975-11983.
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J.Antosiewicz,
M.D.Miller,
K.L.Krause,
and
J.A.McCammon
(1997).
Simulation of electrostatic and hydrodynamic properties of Serratia endonuclease.
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Biopolymers, 41,
443-450.
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J.W.Schwabe
(1997).
The role of water in protein-DNA interactions.
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Curr Opin Struct Biol, 7,
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L.Jen-Jacobson
(1997).
Protein-DNA recognition complexes: conservation of structure and binding energy in the transition state.
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Biopolymers, 44,
153-180.
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M.Sánchez,
P.A.Jennings,
and
C.Murre
(1997).
Conformational changes induced in Hoxb-8/Pbx-1 heterodimers in solution and upon interaction with specific DNA.
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Mol Cell Biol, 17,
5369-5376.
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M.Turmel,
C.Otis,
V.Côté,
and
C.Lemieux
(1997).
Evolutionarily conserved and functionally important residues in the I-CeuI homing endonuclease.
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| |
Nucleic Acids Res, 25,
2610-2619.
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P.J.Heath,
K.M.Stephens,
R.J.Monnat,
and
B.L.Stoddard
(1997).
The structure of I-Crel, a group I intron-encoded homing endonuclease.
|
| |
Nat Struct Biol, 4,
468-476.
|
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PDB code:
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|
|
R.E.Dickerson,
and
T.K.Chiu
(1997).
Helix bending as a factor in protein/DNA recognition.
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| |
Biopolymers, 44,
361-403.
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S.G.Erskine,
G.S.Baldwin,
and
S.E.Halford
(1997).
Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease.
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| |
Biochemistry, 36,
7567-7576.
|
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S.Padmanabhan,
W.Zhang,
M.W.Capp,
C.F.Anderson,
and
M.T.Record
(1997).
Binding of cationic (+4) alanine- and glycine-containing oligopeptides to double-stranded DNA: thermodynamic analysis of effects of coulombic interactions and alpha-helix induction.
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| |
Biochemistry, 36,
5193-5206.
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S.Windolph,
and
J.Alves
(1997).
Influence of divalent cations on inner-arm mutants of restriction endonuclease EcoRI.
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Eur J Biochem, 244,
134-139.
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A.Jeltsch,
C.Wenz,
F.Stahl,
and
A.Pingoud
(1996).
Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme.
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| |
EMBO J, 15,
5104-5111.
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C.R.Robinson,
and
S.G.Sligar
(1996).
Participation of water in Hin recombinase--DNA recognition.
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Protein Sci, 5,
2119-2124.
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F.Stahl,
W.Wende,
A.Jeltsch,
and
A.Pingoud
(1996).
Introduction of asymmetry in the naturally symmetric restriction endonuclease EcoRV to investigate intersubunit communication in the homodimeric protein.
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| |
Proc Natl Acad Sci U S A, 93,
6175-6180.
|
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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.
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Mol Gen Genet, 252,
695-699.
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I.B.Vipond,
B.J.Moon,
and
S.E.Halford
(1996).
An isoleucine to leucine mutation that switches the cofactor requirement of the EcoRV restriction endonuclease from magnesium to manganese.
|
| |
Biochemistry, 35,
1712-1721.
|
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|
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|
|
I.B.Vipond,
and
S.E.Halford
(1996).
Random mutagenesis targeted to the active site of the EcoRV restriction endonuclease.
|
| |
Biochemistry, 35,
1701-1711.
|
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|
|
|
|
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M.J.Haykinson,
L.M.Johnson,
J.Soong,
and
R.C.Johnson
(1996).
The Hin dimer interface is critical for Fis-mediated activation of the catalytic steps of site-specific DNA inversion.
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| |
Curr Biol, 6,
163-177.
|
|
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|
|
M.R.Kurpiewski,
M.Koziolkiewicz,
A.Wilk,
W.J.Stec,
and
L.Jen-Jacobson
(1996).
Chiral phosphorothioates as probes of protein interactions with individual DNA phosphoryl oxygens: essential interactions of EcoRI endonuclease with the phosphate at pGAATTC.
|
| |
Biochemistry, 35,
8846-8854.
|
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|
|
P.K.Wittmayer,
and
R.T.Raines
(1996).
Substrate binding and turnover by the highly specific I-PpoI endonuclease.
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| |
Biochemistry, 35,
1076-1083.
|
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|
|
|
|
|
T.Härd,
and
T.Lundbäck
(1996).
Thermodynamics of sequence-specific protein-DNA interactions.
|
| |
Biophys Chem, 62,
121-139.
|
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X.Qiu,
E.Pohl,
R.K.Holmes,
and
W.G.Hol
(1996).
High-resolution structure of the diphtheria toxin repressor complexed with cobalt and manganese reveals an SH3-like third domain and suggests a possible role of phosphate as co-corepressor.
|
| |
Biochemistry, 35,
12292-12302.
|
|
|
PDB code:
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|
|
J.A.Hirsch,
and
A.K.Aggarwal
(1995).
Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity.
|
| |
EMBO J, 14,
6280-6291.
|
|
|
PDB code:
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Citation data come partly from CiteXplore and partly
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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shown on the right.
|
|
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