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PDBsum entry 1dnk

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protein dna_rna ligands links
Hydrolase/DNA PDB id
1dnk
Jmol
Contents
Protein chain
250 a.a. *
DNA/RNA
Ligands
NAG-NAG
Waters ×77
* Residue conservation analysis
PDB id:
1dnk
Name: Hydrolase/DNA
Title: The x-ray structure of the dnase i-d(ggtatacc)2 complex at 2.3 angstroms resolution
Structure: DNA (5'-d( Gp Gp Tp Ap Tp Ap C)-3'). Chain: b. Engineered: yes. DNA (5'-d( Gp Gp Tp Ap Tp Ap Cp C)-3'). Chain: c. Engineered: yes. Protein (deoxyribonuclease i (dnase i) . Chain: a
Source: Synthetic: yes. Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas. Secretion: milk
Biol. unit: Hexamer (from PQS)
Resolution:
2.30Å     R-factor:   0.188    
Authors: S.A.Weston,A.Lahm,D.Suck
Key ref:
S.A.Weston et al. (1992). X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution. J Mol Biol, 226, 1237-1256. PubMed id: 1518054 DOI: 10.1016/0022-2836(92)91064-V
Date:
10-Aug-92     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00639  (DNAS1_BOVIN) -  Deoxyribonuclease-1
Seq:
Struc:
282 a.a.
250 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.21.1  - Deoxyribonuclease I.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end-products.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     nucleic acid phosphodiester bond hydrolysis   4 terms 
  Biochemical function     hydrolase activity     7 terms  

 

 
DOI no: 10.1016/0022-2836(92)91064-V J Mol Biol 226:1237-1256 (1992)
PubMed id: 1518054  
 
 
X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution.
S.A.Weston, A.Lahm, D.Suck.
 
  ABSTRACT  
 
The crystal structure of a complex between DNase I and the self-complementary octamer duplex d(GGTATACC)2 has been solved using the molecular replacement method and refined to a crystallographic R-factor of 18.8% for all data between 6.0 and 2.3 A resolution. In contrast to the structure of the DNase I-d(GCGATCGC)2 complex solved previously, the DNA remains uncleaved in the crystal. The general architecture of the two complexes is highly similar. DNase I binds in the minor groove of a right-handed DNA duplex, and to the phosphate backbones on either side over five base-pairs, resulting in a widening of the minor groove and a concurrent bend of the DNA away from the bound enzyme. There is very little change in the structure of the DNase I on binding the substrate. Many other features of the interaction are conserved in the two complexes, in particular the stacking of a deoxyribose group of the DNA onto the side-chain of a tyrosine residue (Y76), which affects the DNA conformation and the binding of an arginine side-chain in the minor groove. Although the structures of the DNA molecules appear at first sight rather similar, detailed analysis reveals some differences that may explain the relative resistance of the d(GGTATACC)2 duplex to cleavage by DNase I: whilst some backbone parameters are characteristic of a B-conformation, the spatial orientation of the base-pairs in the d(GGTATACC)2 duplex is close to that generally observed in A-DNA. These results further support the hypothesis that the minor-groove width and depth and the intrinsic flexibility of DNA are the most important parameters affecting the interaction. The disposition of residues around the scissile phosphate group suggests that two histidine residues, H134 and H252, are involved in catalysis.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. (a) View approximately along the helix axis of the Octa V duplex. The central hole, a result of th relatively arge displacement values and reminiscent of canoical A-form DNA is clearly seen. (b) A similar view of an ideal, fibre-drived B-NA of identical sequence is shown fr comparison: no central hole is visible.
Figure 6.
Figure 6. chematic of a possible mechanism for the reaction performed y DNase I. From the dispostion of the esidues and assuming that the reaction involves an in-line ttack at the phosphorus group by a water molecule, t eems most likely that HZ52 acts as a general base o bstrat a proton from a water molecule opposite the 03' atom. The subsequent attack at the phosphorus group with inversio of its configuration gives rise o a penta-ovalent transition state that may be stabilized y the metal ion and possibly by the side-chain of 9. H134 s n n ideal position to protonate the leaving 03'. The metal ion (double circle denoted M++) may also be mportant for the correct positioning of the phosphate roup.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 226, 1237-1256) copyright 1992.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23104058 K.Shi, K.Kurahashi, R.Gao, S.E.Tsutakawa, J.A.Tainer, Y.Pommier, and H.Aihara (2012).
Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
  Nat Struct Mol Biol, 19, 1372-1377.
PDB codes: 4f1h 4f1i 4fpv 4fva 4gew
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
21124947 M.Guéroult, D.Picot, J.Abi-Ghanem, B.Hartmann, and M.Baaden (2010).
How cations can assist DNase I in DNA binding and hydrolysis.
  PLoS Comput Biol, 6, e1001000.  
20686689 W.C.Wong, S.Maurer-Stroh, and F.Eisenhaber (2010).
More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology.
  PLoS Comput Biol, 6, e1000867.  
20185566 Z.Xi, Y.Zhang, R.S.Hegde, Z.Shakked, and D.M.Crothers (2010).
Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA.
  Nucleic Acids Res, 38, 3827-3833.  
19604472 D.S.Glazer, R.J.Radmer, and R.B.Altman (2009).
Improving structure-based function prediction using molecular dynamics.
  Structure, 17, 919-929.  
18252770 A.Matsugami, T.Ohyama, M.Inada, N.Inoue, N.Minakawa, A.Matsuda, and M.Katahira (2008).
Unexpected A-form formation of 4'-thioDNA in solution, revealed by NMR, and the implications as to the mechanism of nuclease resistance.
  Nucleic Acids Res, 36, 1805-1812.
PDB code: 2rmq
18321163 C.N.N'soukpoé-Kossi, and H.A.Tajmir-Riahi (2008).
DNase I-tRNA interaction.
  Oligonucleotides, 18, 65-72.  
17089162 A.Myari, N.Hadjiliadis, A.Garoufis, J.Malina, and V.Brabec (2007).
NMR analysis of duplex d(CGCGATCGCG)2 modified by Lambda- and Delta-[Ru(bpy)2(m-GHK)]Cl2 and DNA photocleavage study.
  J Biol Inorg Chem, 12, 279-292.  
17468836 D.Eulitz, and H.G.Mannherz (2007).
Inhibition of deoxyribonuclease I by actin is to protect cells from premature cell death.
  Apoptosis, 12, 1511-1521.  
17318183 E.P.Carpenter, A.Corbett, H.Thomson, J.Adacha, K.Jensen, J.Bergeron, I.Kasampalidis, R.Exley, M.Winterbotham, C.Tang, G.S.Baldwin, and P.Freemont (2007).
AP endonuclease paralogues with distinct activities in DNA repair and bacterial pathogenesis.
  EMBO J, 26, 1363-1372.
PDB codes: 2jc4 2jc5
17506529 F.A.Tanious, W.Laine, P.Peixoto, C.Bailly, K.D.Goodwin, M.A.Lewis, E.C.Long, M.M.Georgiadis, R.R.Tidwell, and W.D.Wilson (2007).
Unusually strong binding to the DNA minor groove by a highly twisted benzimidazole diphenylether: induced fit and bound water.
  Biochemistry, 46, 6944-6956.  
17889984 Y.Liu, A.Kumar, D.W.Boykin, and W.D.Wilson (2007).
Sequence and length dependent thermodynamic differences in heterocyclic diamidine interactions at AT base pairs in the DNA minor groove.
  Biophys Chem, 131, 1.  
17175542 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: 2ivh 2ivk
16785444 D.Swigon, B.D.Coleman, and W.K.Olson (2006).
Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation.
  Proc Natl Acad Sci U S A, 103, 9879-9884.  
16595670 H.Ago, M.Oda, M.Takahashi, H.Tsuge, S.Ochi, N.Katunuma, M.Miyano, and J.Sakurai (2006).
Structural basis of the sphingomyelin phosphodiesterase activity in neutral sphingomyelinase from Bacillus cereus.
  J Biol Chem, 281, 16157-16167.
PDB codes: 2ddr 2dds 2ddt
16809347 J.S.Hontz, M.T.Villar-Lecumberri, B.M.Potter, M.D.Yoder, L.A.Dreyfus, and J.H.Laity (2006).
Differences in crystal and solution structures of the cytolethal distending toxin B subunit: Relevance to nuclear translocation and functional activation.
  J Biol Chem, 281, 25365-25372.
PDB code: 2f1n
16540594 K.Kaneda, J.Sekiguchi, and T.Shida (2006).
Role of the tryptophan residue in the vicinity of the catalytic center of exonuclease III family AP endonucleases: AP site recognition mechanism.
  Nucleic Acids Res, 34, 1552-1563.  
17034038 X.Hu, and C.E.Stebbins (2006).
Dynamics and assembly of the cytolethal distending toxin.
  Proteins, 65, 843-855.  
16304641 X.Hu, D.Nesic, and C.E.Stebbins (2006).
Comparative structure-function analysis of cytolethal distending toxins.
  Proteins, 62, 421-434.  
16093240 A.E.Openshaw, P.R.Race, H.J.Monzó, J.A.Vázquez-Boland, and M.J.Banfield (2005).
Crystal structure of SmcL, a bacterial neutral sphingomyelinase C from Listeria.
  J Biol Chem, 280, 35011-35017.
PDB code: 1zwx
15626761 C.A.Davis, M.W.Capp, M.T.Record, and R.M.Saecker (2005).
The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase.
  Proc Natl Acad Sci U S A, 102, 285-290.  
16261347 M.Marilley, A.Sanchez-Sevilla, and J.Rocca-Serra (2005).
Fine mapping of inherent flexibility variation along DNA molecules: validation by atomic force microscopy (AFM) in buffer.
  Mol Genet Genomics, 274, 658-670.  
15164065 D.Nesić, Y.Hsu, and C.E.Stebbins (2004).
Assembly and function of a bacterial genotoxin.
  Nature, 429, 429-433.
PDB code: 1sr4
15557256 G.Fuentes, A.Ballesteros, and C.S.Verma (2004).
Specificity in lipases: a computational study of transesterification of sucrose.
  Protein Sci, 13, 3092-3103.  
15557261 M.Seto, M.Whitlow, M.A.McCarrick, S.Srinivasan, Y.Zhu, R.Pagila, R.Mintzer, D.Light, A.Johns, and J.A.Meurer-Ogden (2004).
A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase.
  Protein Sci, 13, 3172-3186.
PDB code: 1x9o
15459284 N.G.Beloglazova, O.O.Kirpota, K.V.Starostin, A.A.Ishchenko, V.I.Yamkovoy, D.O.Zharkov, K.T.Douglas, and G.A.Nevinsky (2004).
Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endonuclease from human placenta.
  Nucleic Acids Res, 32, 5134-5146.  
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Crystal structure of the endonuclease domain encoded by the telomere-specific long interspersed nuclear element, TRAS1.
  J Biol Chem, 279, 41067-41076.
PDB code: 1wdu
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Crystal structure of the targeting endonuclease of the human LINE-1 retrotransposon.
  Structure, 12, 975-986.
PDB code: 1vyb
15044724 W.J.Chen, I.S.Lee, C.Y.Chen, and T.H.Liao (2004).
Biological functions of the disulfides in bovine pancreatic deoxyribonuclease.
  Protein Sci, 13, 875-883.  
15520466 Y.Fukue, N.Sumida, J.Nishikawa, and T.Ohyama (2004).
Core promoter elements of eukaryotic genes have a highly distinctive mechanical property.
  Nucleic Acids Res, 32, 5834-5840.  
15146487 Y.Tsuchiya, K.Kinoshita, and H.Nakamura (2004).
Structure-based prediction of DNA-binding sites on proteins using the empirical preference of electrostatic potential and the shape of molecular surfaces.
  Proteins, 55, 885-894.  
12837780 C.C.Chou, T.W.Lin, C.Y.Chen, and A.H.Wang (2003).
Crystal structure of the hyperthermophilic archaeal DNA-binding protein Sso10b2 at a resolution of 1.85 Angstroms.
  J Bacteriol, 185, 4066-4073.
PDB code: 1udv
12853616 H.G.Abdelhady, S.Allen, M.C.Davies, C.J.Roberts, S.J.Tendler, and P.M.Williams (2003).
Direct real-time molecular scale visualisation of the degradation of condensed DNA complexes exposed to DNase I.
  Nucleic Acids Res, 31, 4001-4005.  
12524450 L.Tian, J.M.Sayer, H.Kroth, G.Kalena, D.M.Jerina, and S.Shuman (2003).
Benzo[a]pyrene-dG adduct interference illuminates the interface of vaccinia topoisomerase with the DNA minor groove.
  J Biol Chem, 278, 9905-9911.  
12843611 T.Obama, S.Fujii, H.Ikezawa, K.Ikeda, M.Imagawa, and K.Tsukamoto (2003).
His151 and His296 are the acid-base catalytic residues of Bacillus cereus sphingomyelinase in sphingomyelin hydrolysis.
  Biol Pharm Bull, 26, 920-926.  
12445335 C.H.Schein, N.Ozgün, T.Izumi, and W.Braun (2002).
Total sequence decomposition distinguishes functional modules, "molegos" in apurinic/apyrimidinic endonucleases.
  BMC Bioinformatics, 3, 37.  
11884629 C.Korn, S.R.Scholz, O.Gimadutdinow, A.Pingoud, and G.Meiss (2002).
Involvement of conserved histidine, lysine and tyrosine residues in the mechanism of DNA cleavage by the caspase-3 activated DNase CAD.
  Nucleic Acids Res, 30, 1325-1332.  
11847288 C.Y.Chen, S.C.Lu, and T.H.Liao (2002).
The distinctive functions of the two structural calcium atoms in bovine pancreatic deoxyribonuclease.
  Protein Sci, 11, 659-668.  
12429100 G.J.Ostheimer, A.Barkan, and B.W.Matthews (2002).
Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins.
  Structure, 10, 1593-1601.
PDB code: 1ln4
12235390 H.L.Ng, and R.E.Dickerson (2002).
Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG.
  Nucleic Acids Res, 30, 4061-4067.  
12016307 K.S.Murakami, S.Masuda, E.A.Campbell, O.Muzzin, and S.A.Darst (2002).
Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex.
  Science, 296, 1285-1290.
PDB code: 1l9z
11861910 Z.Morávek, S.Neidle, and B.Schneider (2002).
Protein and drug interactions in the minor groove of DNA.
  Nucleic Acids Res, 30, 1182-1191.  
11294633 J.F.Goossens, E.Bouey-Bencteux, R.Houssin, J.P.Hénichart, P.Colson, C.Houssier, W.Laine, B.Baldeyrou, and C.Bailly (2001).
DNA interaction of the tyrosine protein kinase inhibitor PD153035 and its N-methyl analogue.
  Biochemistry, 40, 4663-4671.  
11328878 X.Wang, and R.T.Simpson (2001).
Chromatin structure mapping in Saccharomyces cerevisiae in vivo with DNase I.
  Nucleic Acids Res, 29, 1943-1950.  
10688897 H.L.Ng, M.L.Kopka, and R.E.Dickerson (2000).
The structure of a stable intermediate in the A <--> B DNA helix transition.
  Proc Natl Acad Sci U S A, 97, 2035-2039.
PDB code: 1dc0
10828058 J.M.Holopainen, O.P.Medina, A.J.Metso, and P.K.Kinnunen (2000).
Sphingomyelinase activity associated with human plasma low density lipoprotein.
  J Biol Chem, 275, 16484-16489.  
10823942 K.Hofmann, S.Tomiuk, G.Wolff, and W.Stoffel (2000).
Cloning and characterization of the mammalian brain-specific, Mg2+-dependent neutral sphingomyelinase.
  Proc Natl Acad Sci U S A, 97, 5895-5900.  
10692410 K.Klumpp, L.Doan, N.A.Roberts, and B.Handa (2000).
RNA and DNA hydrolysis are catalyzed by the influenza virus endonuclease.
  J Biol Chem, 275, 6181-6188.  
10931312 K.Kobryn, D.Z.Naigamwalla, and G.Chaconas (2000).
Site-specific DNA binding and bending by the Borrelia burgdorferi Hbb protein.
  Mol Microbiol, 37, 145-155.  
10648607 S.Christensen, G.Pont-Kingdon, and D.Carroll (2000).
Target specificity of the endonuclease from the Xenopus laevis non-long terminal repeat retrotransposon, Tx1L.
  Mol Cell Biol, 20, 1219-1226.  
10832103 Y.Mizutani, K.Tamiya-Koizumi, F.Irie, Y.Hirabayashi, M.Miwa, and S.Yoshida (2000).
Cloning and expression of rat neutral sphingomyelinase: enzymological characterization and identification of essential histidine residues.
  Biochim Biophys Acta, 1485, 236-246.  
10410797 C.D.Mol, S.S.Parikh, C.D.Putnam, T.P.Lo, and J.A.Tainer (1999).
DNA repair mechanisms for the recognition and removal of damaged DNA bases.
  Annu Rev Biophys Biomol Struct, 28, 101-128.  
  10493579 C.Q.Pan, and R.A.Lazarus (1999).
Ca2+-dependent activity of human DNase I and its hyperactive variants.
  Protein Sci, 8, 1780-1788.  
10413462 J.Greenwald, V.Le, S.L.Butler, F.D.Bushman, and S.Choe (1999).
The mobility of an HIV-1 integrase active site loop is correlated with catalytic activity.
  Biochemistry, 38, 8892-8898.
PDB codes: 1b92 1b9d 1b9f
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
9917068 M.Sette, R.Spurio, P.van Tilborg, C.O.Gualerzi, and R.Boelens (1999).
Identification of the ribosome binding sites of translation initiation factor IF3 by multidimensional heteronuclear NMR spectroscopy.
  RNA, 5, 82-92.  
10194301 S.J.Evans, E.J.Shipstone, W.N.Maughan, and B.A.Connolly (1999).
Site-directed mutagenesis of phosphate-contacting amino acids of bovine pancreatic deoxyribonuclease I.
  Biochemistry, 38, 3902-3909.  
  9541395 C.Q.Pan, J.S.Ulmer, A.Herzka, and R.A.Lazarus (1998).
Mutational analysis of human DNase I at the DNA binding interface: implications for DNA recognition, catalysis, and metal ion dependence.
  Protein Sci, 7, 628-636.  
9565591 C.Q.Pan, and R.A.Lazarus (1998).
Hyperactivity of human DNase I variants. Dependence on the number of positively charged residues and concentration, length, and environment of DNA.
  J Biol Chem, 273, 11701-11708.  
9660804 C.Q.Pan, T.H.Dodge, D.L.Baker, W.S.Prince, D.V.Sinicropi, and R.A.Lazarus (1998).
Improved potency of hyperactive and actin-resistant human DNase I variants for treatment of cystic fibrosis and systemic lupus erythematosus.
  J Biol Chem, 273, 18374-18381.  
9694826 H.Torrance, W.Giffin, D.J.Rodda, L.Pope, and R.J.Haché (1998).
Sequence-specific binding of Ku autoantigen to single-stranded DNA.
  J Biol Chem, 273, 20810-20819.  
9705308 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: 1bgb
9512546 P.König, L.Fairall, and D.Rhodes (1998).
Sequence-specific DNA recognition by the myb-like domain of the human telomere binding protein TRF1: a model for the protein-DNA complex.
  Nucleic Acids Res, 26, 1731-1740.  
9843516 S.Cal, K.L.Tan, A.McGregor, and B.A.Connolly (1998).
Conversion of bovine pancreatic DNase I to a repair endonuclease with a high selectivity for abasic sites.
  EMBO J, 17, 7128-7138.  
9184142 C.Q.Pan, and R.A.Lazarus (1997).
Engineering hyperactive variants of human deoxyribonuclease I by altering its functional mechanism.
  Biochemistry, 36, 6624-6632.  
9782777 D.Suck (1997).
DNA recognition by structure-selective nucleases.
  Biopolymers, 44, 405-421.  
9030776 E.Tuite, U.Sehlstedt, P.Hagmar, B.Nordén, and M.Takahashi (1997).
Effects of minor and major groove-binding drugs and intercalators on the DNA association of minor groove-binding proteins RecA and deoxyribonuclease I detected by flow linear dichroism.
  Eur J Biochem, 243, 482-492.  
9082984 H.J.Kwon, R.Tirumalai, A.Landy, and T.Ellenberger (1997).
Flexibility in DNA recombination: structure of the lambda integrase catalytic core.
  Science, 276, 126-131.
PDB code: 1ae9
9080779 J.Antosiewicz, M.D.Miller, K.L.Krause, and J.A.McCammon (1997).
Simulation of electrostatic and hydrodynamic properties of Serratia endonuclease.
  Biopolymers, 41, 443-450.  
9351835 M.A.Gorman, S.Morera, D.G.Rothwell, E.de La Fortelle, C.D.Mol, J.A.Tainer, I.D.Hickson, and P.S.Freemont (1997).
The crystal structure of the human DNA repair endonuclease HAP1 suggests the recognition of extra-helical deoxyribose at DNA abasic sites.
  EMBO J, 16, 6548-6558.
PDB code: 1bix
9097733 M.C.Wahl, and M.Sundaralingam (1997).
Crystal structures of A-DNA duplexes.
  Biopolymers, 44, 45-63.  
9395327 Y.M.Hsiao, H.C.Ho, W.Y.Wang, M.F.Tam, and T.H.Liao (1997).
Purification and characterization of tilapia (Oreochromis mossambicus) deoxyribonuclease I--primary structure and cDNA sequence.
  Eur J Biochem, 249, 786-791.  
8756512 A.H.Elcock, A.Rodger, and W.G.Richards (1996).
Theoretical studies of the intercalation of 9-hydroxyellipticine in DNA.
  Biopolymers, 39, 309-326.  
8805594 C.Davies, V.Ramakrishnan, and S.W.White (1996).
Structural evidence for specific S8-RNA and S8-protein interactions within the 30S ribosomal subunit: ribosomal protein S8 from Bacillus stearothermophilus at 1.9 A resolution.
  Structure, 4, 1093-1104.
PDB code: 1sei
8987994 D.Hüsken, G.Goodall, M.J.Blommers, W.Jahnke, J.Hall, R.Häner, and H.E.Moser (1996).
Creating RNA bulges: cleavage of RNA in RNA/DNA duplexes by metal ion catalysis.
  Biochemistry, 35, 16591-16600.  
8772379 F.Martín, M.Olivares, M.C.López, and C.Alonso (1996).
Do non-long terminal repeat retrotransposons have nuclease activity?
  Trends Biochem Sci, 21, 283-285.  
8679635 H.Thorogood, T.R.Waters, A.W.Parker, C.W.Wharton, and B.A.Connolly (1996).
Resonance Raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV.
  Biochemistry, 35, 8723-8733.  
8710851 J.S.Ulmer, A.Herzka, K.J.Toy, D.L.Baker, A.H.Dodge, D.Sinicropi, S.Shak, and R.A.Lazarus (1996).
Engineering actin-resistant human DNase I for treatment of cystic fibrosis.
  Proc Natl Acad Sci U S A, 93, 8225-8229.  
8679636 L.Cummins, D.Graff, G.Beaton, W.S.Marshall, and M.H.Caruthers (1996).
Biochemical and physicochemical properties of phosphorodithioate DNA.
  Biochemistry, 35, 8734-8741.  
8663567 M.Dlakic, K.Park, J.D.Griffith, S.C.Harvey, and R.E.Harrington (1996).
The organic crystallizing agent 2-methyl-2,4-pentanediol reduces DNA curvature by means of structural changes in A-tracts.
  J Biol Chem, 271, 17911-17919.  
8632978 M.Dlakić, and R.E.Harrington (1996).
The effects of sequence context on DNA curvature.
  Proc Natl Acad Sci U S A, 93, 3847-3852.  
8758988 P.Friedhoff, B.Kolmes, O.Gimadutdinow, W.Wende, K.L.Krause, and A.Pingoud (1996).
Analysis of the mechanism of the Serratia nuclease using site-directed mutagenesis.
  Nucleic Acids Res, 24, 2632-2639.  
8557624 S.Cal, and B.A.Connolly (1996).
The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition sequence GATATC.
  J Biol Chem, 271, 1008-1015.  
8718874 S.Cal, R.G.Nicieza, B.A.Connolly, and J.Sánchez (1996).
Interaction of the periplasmic dG-selective Streptomyces antibioticus nuclease with oligodeoxynucleotide substrates.
  Biochemistry, 35, 10828-10836.  
  8976554 Y.Matsuo, A.Yamada, K.Tsukamoto, H.Tamura, H.Ikezawa, H.Nakamura, and K.Nishikawa (1996).
A distant evolutionary relationship between bacterial sphingomyelinase and mammalian DNase I.
  Protein Sci, 5, 2459-2467.  
7731789 A.D.Baxevanis, S.H.Bryant, and D.Landsman (1995).
Homology model building of the HMG-1 box structural domain.
  Nucleic Acids Res, 23, 1019-1029.  
  7744018 C.Bailly, N.E.Møllegaard, P.E.Nielsen, and M.J.Waring (1995).
The influence of the 2-amino group of guanine on DNA conformation. Uranyl and DNase I probing of inosine/diaminopurine substituted DNA.
  EMBO J, 14, 2121-2131.  
  7737131 I.Brukner, R.Sánchez, D.Suck, and S.Pongor (1995).
Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.
  EMBO J, 14, 1812-1818.  
  7828582 J.A.Stamatoyannopoulos, A.Goodwin, T.Joyce, and C.H.Lowrey (1995).
NF-E2 and GATA binding motifs are required for the formation of DNase I hypersensitive site 4 of the human beta-globin locus control region.
  EMBO J, 14, 106-116.  
7876117 K.A.Latham, J.S.Taylor, and R.S.Lloyd (1995).
T4 endonuclease V protects the DNA strand opposite a thymine dimer from cleavage by the footprinting reagents DNase I and 1,10-phenanthroline-copper.
  J Biol Chem, 270, 3765-3771.  
8533156 L.H.Pearl, and R.Savva (1995).
DNA repair in three dimensions.
  Trends Biochem Sci, 20, 421-426.  
7647248 M.A.Young, G.Ravishanker, D.L.Beveridge, and H.M.Berman (1995).
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes.
  Biophys J, 68, 2454-2468.  
7826675 D.Suck (1994).
DNA recognition by DNase I.
  J Mol Recognit, 7, 65-70.  
  7957064 M.Lavigne, A.Kolb, E.Yeramian, and H.Buc (1994).
CRP fixes the rotational orientation of covalently closed DNA molecules.
  EMBO J, 13, 4983-4990.  
7937076 P.Carrera, and F.Azorín (1994).
Structural characterization of intrinsically curved AT-rich DNA sequences.
  Nucleic Acids Res, 22, 3671-3680.  
8078761 P.Friedhoff, O.Gimadutdinow, and A.Pingoud (1994).
Identification of catalytically relevant amino acids of the extracellular Serratia marcescens endonuclease by alignment-guided mutagenesis.
  Nucleic Acids Res, 22, 3280-3287.  
7763979 J.A.Tainer, and R.P.Cunningham (1993).
Molecular recognition in DNA-binding proteins and enzymes.
  Curr Opin Biotechnol, 4, 474-483.  
1336176 K.R.Fox (1992).
Probing the conformations of eight cloned DNA dodecamers; CGCGAATTCGCG, CGCGTTAACGCG, CGCGTATACGCG, CGCGATATCGCG, CGCAAATTTGCG, CGCTTTAAAGCG, CGCGGATCCGCG and CGCGGTACCGCG.
  Nucleic Acids Res, 20, 6487-6493.  
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.