Metal Activation of Enzymes in Nucleic Acid Biochemistry

Reverse Transcriptase Motifs in the Catalytic Subunit of Telomerase

Lingner, J., Hughes, T. R., Shevchenko, A., Mann, M., Lundblad, V., & Cech, T. R. (1997) · Science · doi:10.1126/science.276.5312.561 · Cited by 1,269

A general two-metal-ion mechanism for catalytic RNA

Steitz, T. A., & Steitz, J. A. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.14.6498 · Cited by 1,171

Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism.

Beese, L. S., & Steitz, T. A. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07917.x · Cited by 1,048

Binuclear Metallohydrolases

Wilcox, D. E. (1996) · Chemical Reviews · doi:10.1021/cr950043b · Cited by 893

STRUCTURES OF TERNARY COMPLEXES OF RAT DNA POLYMERASE BETA, A DNA TEMPLATE-PRIMER, AND DDCTP: 2bpf

Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., & Kraut, J. (1994) · Worldwide Protein Data Bank · doi:10.2210/pdb2bpf/pdb · Cited by 692

FUNCTION AND STRUCTURE RELATIONSHIPS IN DNA POLYMERASES

Joyce, C. M., & Steitz, T. A. (1994) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.63.070194.004021 · Cited by 619

Carboxypeptidase A

Christianson, D. W., & Lipscomb, W. N. (1989) · Accounts of Chemical Research · doi:10.1021/ar00158a003 · Cited by 606

Structures of Ternary Complexes of Rat DNA Polymerase β, a DNA Template-Primer, and ddCTP

Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., & Kraut, J. (1994) · Science · doi:10.1126/science.7516580 · Cited by 598

Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase

Davies, J. F., Hostomska, Z., Hostomsky, Z., Jordan, S. R., & Matthews, D. A. (1991) · Science · doi:10.1126/science.1707186 · Cited by 570

Separate domains of p21 involved in the inhibition of Cdk kinase and PCNA

Chen, J., Jackson, P. K., Kirschner, M. W., & Dutta, A. (1995) · Nature · doi:10.1038/374386a0 · Cited by 548

Crystal Structure of Rat DNA Polymerase β: Evidence for a Common Polymerase Mechanism

Sawaya, M. R., Pelletier, H., Kumar, A., Wilson, S. H., & Kraut, J. (1994) · Science · doi:10.1126/science.7516581 · Cited by 469

Prevention of Islet Allograft Rejection with Engineered Myoblasts Expressing FasL in Mice

Lau, H. T., Yu, M., Fontana, A., & Stoeckert, C. J. (1996) · Science · doi:10.1126/science.273.5271.109 · Cited by 445

Structure of a unique binuclear manganese cluster in arginase

Kanyo, Z. F., Scolnick, L. R., Ash, D. E., & Christianson, D. W. (1996) · Nature · doi:10.1038/383554a0 · Cited by 441

Metal ion catalysis in the Tetrahymena ribozyme reaction

Piccirilli, J. A., Vyle, J. S., Caruthers, M. H., & Cech, T. R. (1993) · Nature · doi:10.1038/361085a0 · Cited by 385

Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA.

Quigley, G. J., Teeter, M. M., & Rich, A. (1978) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.75.1.64 · Cited by 381

Staphylococcal nuclease: Proposed mechanism of action based on structure of enzyme—thymidine 3′,5′-bisphosphate—calcium ion complex at 1.5-Å resolution

Cotton, F. A., Hazen, E. E., & Legg, M. J. (1979) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.76.6.2551 · Cited by 377

Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution

Sousa, R., Chung, Y. J., Rose, J. P., & Wang, B.-C. (1993) · Nature · doi:10.1038/364593a0 · Cited by 361

Three-dimensional structure of ribonuclease H from E. coli

Katayanagi, K., Miyagawa, M., Matsushima, M., Ishikawa, M., Kanaya, S., Ikehara, M., Matsuzaki, T., & Morikawa, K. (1990) · Nature · doi:10.1038/347306a0 · Cited by 349

Recognition and Cleavage of DNA by Type‐II Restriction Endonucleases

Pingoud, A., & Jeltsch, A. (1997) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1997.t01-6-00001.x · Cited by 330

Novel subunit—subunit interactions in the structure of glutamine synthetase

Almassy, R. J., Janson, C. A., Hamlin, R., Xuong, N.-H., & Eisenberg, D. (1986) · Nature · doi:10.1038/323304a0 · Cited by 303

Structure of Bam HI Endonuclease Bound to DNA: Partial Folding and Unfolding on DNA Binding

Newman, M., Strzelecka, T., Dorner, L. F., Schildkraut, I., & Aggarwal, A. K. (1995) · Science · doi:10.1126/science.7624794 · Cited by 298

Effect of manganese ions on the incorporation of dideoxynucleotides by bacteriophage T7 DNA polymerase and Escherichia coli DNA polymerase I.

Tabor, S., & Richardson, C. C. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.11.4076 · Cited by 288

Atomic structure of the RuvC resolvase: A holliday junction-specific endonuclease from E. coli

Ariyoshi, M., Vassylyev, D. G., Iwasaki, H., Nakamura, H., Shinagawa, H., & Morikawa, K. (1994) · Cell · doi:10.1016/0092-8674(94)90280-1 · Cited by 283

A Unified Polymerase Mechanism for Nonhomologous DNA and RNA Polymerases

Steitz, T. A., Smerdon, S. J., Jäger, J., & Joyce, C. M. (1994) · Science · doi:10.1126/science.7528445 · Cited by 280

Exonuclease III and endonuclease IV remove 3' blocks from DNA synthesis primers in H2O2-damaged Escherichia coli.

Demple, B., Johnson, A., & Fung, D. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.20.7731 · Cited by 275

Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.

Volbeda, A., Lahm, A., Sakiyama, F., & Suck, D. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07683.x · Cited by 258

Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution

Katayanagi, K., Miyagawa, M., Matsushima, M., Ishikawa, M., Kanaya, S., Nakamura, H., Ikehara, M., Matsuzaki, T., & Morikawa, K. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)90260-q · Cited by 224

Structure of the bacteriophage Mu transposase core: A common structural motif for DNA transposition and retroviral integration

Rice, P., & Kiyoshi, M. (1995) · Cell · doi:10.1016/0092-8674(95)90308-9 · Cited by 222

Mg2+ Binding to the Active Site of EcoRV Endonuclease: A Crystallographic Study of Complexes with Substrate and Product DNA at 2-.ANG. Resolution

Kostrewa, D., & Winkler, F. K. (1995) · Biochemistry · doi:10.1021/bi00002a036 · Cited by 221

Structure of PvuII endonuclease with cognate DNA.

Cheng, X., Balendiran, K., Schildkraut, I., & Anderson, J. E. (1994) · The EMBO Journal · doi:10.1002/j.1460-2075.1994.tb06708.x · Cited by 205

Structure and function of restriction endonucleases

Aggarwal, A. K. (1995) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(95)80004-k · Cited by 200

A unique mechanism for RNA catalysis: the role of metal cofactors in hairpin ribozyme cleavage

Hampel, A., & Cowan, J. A. (1997) · Chemistry & Biology · doi:10.1016/s1074-5521(97)90323-9 · Cited by 194

A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease

Ceska, T. A., Sayers, J. R., Stier, G., & Suck, D. (1996) · Nature · doi:10.1038/382090a0 · Cited by 187

Structure of Bacteriophage T4 RNase H, a 5′ to 3′ RNA–DNA and DNA–DNA Exonuclease with Sequence Similarity to the RAD2 Family of Eukaryotic Proteins

Mueser, T. C., Nossal, N. G., & Hyde, C. C. (1996) · Cell · doi:10.1016/s0092-8674(00)81310-0 · Cited by 178

The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations

Bujacz, G., Jaskólski, M., Alexandratos, J., Wlodawer, A., Merkel, G., Katz, R. A., & Skalka, A. M. (1996) · Structure · doi:10.1016/s0969-2126(96)00012-3 · Cited by 170

Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate

Beese, L. S., Friedman, J. M., & Steitz, T. A. (1993) · Biochemistry · doi:10.1021/bi00214a004 · Cited by 170

Effects of functional group changes in the EcoRI recognition site on the cleavage reaction catalyzed by the endonuclease

McLaughlin, L. W., Benseler, F., Graeser, E., Piel, N., & Scholtissek, S. (1987) · Biochemistry · doi:10.1021/bi00397a007 · Cited by 168

2.3 Å crystal structure of the catalytic domain of DNA polymerase β

Davies, J. F., Almassy, R. J., Hostomska, Z., Ferre, R. A., & Hostomsky, Z. (1994) · Cell · doi:10.1016/0092-8674(94)90388-3 · Cited by 168

Construction of a plasmid that overproduces the large proteolytic fragment (Klenow fragment) of DNA polymerase I of Escherichia coli.

Joyce, C. M., & Grindley, N. D. (1983) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.80.7.1830 · Cited by 167

Native Recombinant Cyclophilins A, B, and C Degrade DNA Independently of Peptidylprolyl cis-trans-Isomerase Activity

Montague, J. W., Hughes, F. M., & Cidlowski, J. A. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.10.6677 · Cited by 162

Mapping of Catalytic Residues in the RNA Polymerase Active Center

Zaychikov, E., Martin, E., Denissova, L., Kozlov, M., Markovtsov, V., Kashlev, M., Heumann, H., Nikiforov, V., Goldfarb, A., & Mustaev, A. (1996) · Science · doi:10.1126/science.273.5271.107 · Cited by 159

Free energy relationships in metalloenzyme-catalyzed reactions. Calculations of the effects of metal ion substitutions in staphylococcal nuclease

Aaqvist, J., & Warshel, A. (1990) · Journal of the American Chemical Society · doi:10.1021/ja00164a003 · Cited by 158

Enzymes in DNA Metabolism

Richardson, C. C. (1969) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.38.070169.004051 · Cited by 149

Molecular Mapping and Detoxification of the Lipid A Binding Site by Synthetic Peptides

Rustici, A., Velucchi, M., Faggioni, R., Sironi, M., Ghezzi, P., Quataert, S. A., Green, B., & Porro, M. (1993) · Science · doi:10.1126/science.8420003 · Cited by 144

Crystal structure of Escherichia coli RNase HI in complex with Mg2+ at 2.8 Å resolution: Proof for a single Mg2+‐binding site

Katayanagi, K., Okumura, M., & Morikawa, K. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340170402 · Cited by 136

Ca2+Mg2+-dependent nuclease: Tissue distribution, relationship to inter-nucleosomal DNA fragmentation and inhibition by Zn2+

Giannakis, C., Forbes, I. J., & Zalewski, P. D. (1991) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(91)91278-k · Cited by 127

Calcium(II) site specificity: effect of size and charge on metal ion binding to an EF-hand-like site

Snyder, E. E., Buoscio, B. W., & Falke, J. J. (1990) · Biochemistry · doi:10.1021/bi00468a021 · Cited by 123

Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes.

Jeltsch, A., Alves, J., Wolfes, H., Maass, G., & Pingoud, A. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.18.8499 · Cited by 116

Analysis of the Mechanism of the Serratia Nuclease Using Site-Directed Mutagenesis

Friedhoff, P., Kolmes, B., Gimadutdinow, O., Wende, W., Krause, K. L., & Pingoud, A. M. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.14.2632 · Cited by 98

A Metal-induced Conformational Change and Activation of HIV-1 Integrase

Asante‐Appiah, E., & Skalka, A. M. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.26.16196 · Cited by 87

Mutation of the aspartic acid residues of the GDD sequence motif of poliovirus RNA-dependent RNA polymerase results in enzymes with altered metal ion requirements for activity

Jablonski, S. A., & Morrow, C. D. (1995) · Journal of Virology · doi:10.1128/jvi.69.3.1532-1539.1995 · Cited by 85

Studies on Polynucleotides

van de Sande, J. H., Loewen, P. C., & Khorana, H. G. (1972) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)44775-3 · Cited by 77

Novel ion specificity of a carboxylate cluster magnesium(II) binding site: Strong charge selectivity and weak size selectivity

Needham, J. V., Chen, T. Y., & Falke, J. J. (1993) · Biochemistry · doi:10.1021/bi00064a020 · Cited by 77

Divalent cation modulation of the ribonuclease functions of human immunodeficiency virus reverse transcriptase

Cirino, N. M., Cameron, C. E., Smith, J. S., Roth, M. J., Benkovic, S. J., & Grice, S. F. J. L. (1995) · Biochemistry · doi:10.1021/bi00031a016 · Cited by 75

X‐Ray Structure of Yeast Inorganic Pyrophosphatase Complexed with Manganese and Phosphate

Harutyunyan, E. H., Kuranova, I. P., Vainshtein, B. K., Höhne, W. E., Lamzin, V. S., Dauter, Z., Teplyakov, A., & Wilson, K. S. (1996) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1996.0220u.x · Cited by 74

Rapid Reaction Analysis of the Catalytic Cycle of the EcoRV Restriction Endonuclease

Baldwin, G. S., Vipond, I. B., & Halford, S. E. (1995) · Biochemistry · doi:10.1021/bi00002a038 · Cited by 69

E. coli DNA polymerase I as a reverse transcriptase.

Ricchetti, M., & BUC, H. C. (1993) · The EMBO Journal · doi:10.1002/j.1460-2075.1993.tb05670.x · Cited by 67

Kinetic and Stoichiometric Analysis for the Binding of Escherichia coli Ribonuclease HI to RNA-DNA Hybrids Using Surface Plasmon Resonance

Haruki, M., Noguchi, E., Kanaya, S., & Crouch, R. J. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.35.22015 · Cited by 65

Proteolytic Dissection of Zab, the Z-DNA-binding Domain of Human ADAR1

Schwartz, T., Lowenhaupt, K., Kim, Y., Li, L., Brown, B. A., Herbert, A. G., & Rich, A. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.5.2899 · Cited by 64

On the catalytic mechanism of EcoRI and EcoRV A detailed proposal based on biochemical results, structural data and molecular modelling

Jeltsch, A., Alves, J., Maaß, G., & Pingoud, A. M. (1992) · FEBS Letters · doi:10.1016/0014-5793(92)80576-3 · Cited by 64

Metal binding to DNA polymerase I, its large fragment, and two 3‘,5‘-exonuclease mutants of the large fragment.

Mullen, G. P., SERPERSU, E. H., Ferrin, L. J., Loeb, L. A., & Mildvan, A. S. (1990) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)77304-3 · Cited by 59

Quantitating and engineering the ion specificity of an EF-hand-like calcium binding site

Falke, J. J., Snyder, E. E., Thatcher, K. C., & Voertler, C. S. (1991) · Biochemistry · doi:10.1021/bi00099a029 · Cited by 56

Glutamine 151 participates in the substrate dNTP binding function of HIV-1 reverse transcriptase

Sarafianos, S. G., Pandey, V. N., Kaushik, N., & Modak, M. J. (1995) · Biochemistry · doi:10.1021/bi00021a036 · Cited by 56

Metallobiochemistry of magnesium. Coordination complexes with biological substrates: site specificity, kinetics and thermodynamics of binding, and implications for activity

Cowan, J. A. (1991) · Inorganic Chemistry · doi:10.1021/ic00013a008 · Cited by 56

Quantitative Evaluation of Electrostatic and Hydrogen-Bonding Contributions to Metal Cofactor Binding to Nucleic Acids

Black, C. B., & Cowan, J. A. (1994) · Journal of the American Chemical Society · doi:10.1021/ja00083a002 · Cited by 41

Polymerase Structures and Mechanism

Pelletier, H. (1994) · Science · doi:10.1126/science.7801132 · Cited by 40

Crystal structures of ribonuclease HI active site mutants from Escherichia coli.

Katayanagi, K., Ishikawa, M., Okumura, M., Ariyoshi, M., Kanaya, S., Kawano, Y., Suzuki, M., Tanaka, I., & Morikawa, K. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(20)80652-8 · Cited by 37

Proposal for new catalytic roles for two invariant residues in Escherichia coli ribonuclease HI

Kashiwagi, T., Jeanteur, D., Haruki, M., Katayanagi, K., Kanaya, S., & Morikawa, K. (1996) · Protein Engineering Design and Selection · doi:10.1093/protein/9.10.857 · Cited by 35

Magnesium Activation of Ribonuclease H. Evidence for One Catalytic Metal Ion

Black, C. B., & Cowan, J. A. (1994) · Inorganic Chemistry · doi:10.1021/ic00103a030 · Cited by 33

The Embedded Ribonucleotide Assay: A Chimeric Substrate for Studying Cleavage of RNA by Transesterification

Jenkins, L. A., Bashkin, J. K., & Autry, M. E. (1996) · Journal of the American Chemical Society · doi:10.1021/ja960191z · Cited by 30

Inert Chromium and Cobalt Complexes as Probes of Magnesium‐Dependent Enzymes

Black, C. B., & Cowan, J. A. (1997) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1997.00684.x · Cited by 27

Metal-mediated hydrolysis of biological phosphate esters

Cowan, J. A. (1997) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s007750050121 · Cited by 26

Rational Redesign of a Metal-Dependent Nuclease. Engineering the Active Site of Magnesium-Dependent Ribonuclease H To Form an Active "Metal-Independent" Enzyme

Casareno, R. L. B., Li, D., & Cowan, J. A. (1995) · Journal of the American Chemical Society · doi:10.1021/ja00149a026 · Cited by 23

Differential Effects of Moloney Murine Leukemia Virus Reverse Transcriptase Mutations on RNase H Activity in Mg2+ and Mn2+

Blain, S. W., & Goff, S. P. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.3.1448 · Cited by 20

Properties of the 5'.fwdarw.3' Exonuclease/Ribonuclease H Activity of Thermus thermophilus DNA Polymerase

Auer, T., Landre, P., & Myers, T. W. (1995) · Biochemistry · doi:10.1021/bi00015a010 · Cited by 12

Mechanism of metal-promoted catalysis of nucleic acid hydrolysis by Escherichia coli ribonuclease H

Black, C. B., Foster, M. P., & Cowan, J. A. (1996) · JBIC Journal of Biological Inorganic Chemistry · doi:10.1007/s007750050084 · Cited by 11

Structure and function of type II restriction endonucleases

Pingoud, A. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.18.3705 · Cited by 639

Structural and catalytic chemistry of magnesium-dependent enzymes

Cowan, J. A. (2002) · Biometals · doi:10.1023/a:1016022730880 · Cited by 428

The major human abasic endonuclease: formation, consequences and repair of abasic lesions in DNA

Wilson, D. M., & Barsky, D. (2001) · Mutation Research/DNA Repair · doi:10.1016/s0921-8777(01)00063-5 · Cited by 408

Quantum Chemical Studies of Intermediates and Reaction Pathways in Selected Enzymes and Catalytic Synthetic Systems

Noodleman, L., Lovell, T., Han, W.-G., Li, J., & Himo, F. (2004) · Chemical Reviews · doi:10.1021/cr020625a · Cited by 373

Can a Hydroxide Ligand Trigger a Change in the Coordination Number of Magnesium Ions in Biological Systems?

Kluge, S., & Weston, J. (2005) · Biochemistry · doi:10.1021/bi047454j · Cited by 56