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Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c (1992)

H. Pelletier ; J. Kraut

American Association for the Advancement of Science (AAAS)

In: Science. 258(5089): 1748-55.

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Publication Date: 1992-12-11

Description: The crystal structure of a 1:1 complex between yeast cytochrome c peroxidase and yeast iso-1-cytochrome c was determined at 2.3 A resolution. This structure reveals a possible electron transfer pathway unlike any previously proposed for this extensively studied redox pair. The shortest straight line between the two hemes closely follows the peroxidase backbone chain of residues Ala194, Ala193, Gly192, and finally Trp191, the indole ring of which is perpendicular to, and in van der Waals contact with, the peroxidase heme. The crystal structure at 2.8 A of a complex between yeast cytochrome c peroxidase and horse heart cytochrome c was also determined. Although crystals of the two complexes (one with cytochrome c from yeast and the other with cytochrome c from horse) grew under very different conditions and belong to different space groups, the two complex structures are closely similar, suggesting that cytochrome c interacts with its redox partners in a highly specific manner.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pelletier, H -- Kraut, J -- DK07233/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 1992 Dec 11;258(5089):1748-55.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego, La Jolla 92093-0317.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1334573" target="_blank"〉PubMed〈/a〉

Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Cytochrome c Group/*chemistry/metabolism ; Cytochrome-c Peroxidase/*chemistry/metabolism ; *Electron Transport ; Heme/metabolism ; Horses ; Models, Molecular ; Molecular Sequence Data ; *Protein Conformation ; Saccharomyces cerevisiae/metabolism ; X-Ray Diffraction/methods

Print ISSN: 0036-8075

Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

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Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP (1994)

H. Pelletier ; M. R. Sawaya ; A. Kumar ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 264(5167): 1891-903.

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Publication Date: 1994-06-24

Description: Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA template-primer, and dideoxycytidine triphosphate (ddCTP) have been determined at 2.9 A and 3.6 A resolution, respectively. ddCTP is the triphosphate of dideoxycytidine (ddC), a nucleoside analog that targets the reverse transcriptase of human immunodeficiency virus (HIV) and is at present used to treat AIDS. Although crystals of the two complexes belong to different space groups, the structures are similar, suggesting that the polymerase-DNA-ddCTP interactions are not affected by crystal packing forces. In the pol beta active site, the attacking 3'-OH of the elongating primer, the ddCTP phosphates, and two Mg2+ ions are all clustered around Asp190, Asp192, and Asp256. Two of these residues, Asp190 and Asp256, are present in the amino acid sequences of all polymerases so far studied and are also spatially similar in the four polymerases--the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta--whose crystal structures are now known. A two-metal ion mechanism is described for the nucleotidyl transfer reaction and may apply to all polymerases. In the ternary complex structures analyzed, pol beta binds to the DNA template-primer in a different manner from that recently proposed for other polymerase-DNA models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pelletier, H -- Sawaya, M R -- Kumar, A -- Wilson, S H -- Kraut, J -- CA17374/CA/NCI NIH HHS/ -- ES06839/ES/NIEHS NIH HHS/ -- GM10928/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jun 24;264(5167):1891-903.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego 92093-0317.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7516580" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; DNA Polymerase I/*chemistry/metabolism ; DNA Primers/*chemistry/metabolism ; DNA-Directed RNA Polymerases/chemistry/metabolism ; Deoxycytosine Nucleotides/*chemistry/metabolism ; Dideoxynucleotides ; HIV Reverse Transcriptase ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; RNA-Directed DNA Polymerase/chemistry/metabolism ; Rats ; Recombinant Proteins ; Templates, Genetic ; Thymine Nucleotides/chemistry/metabolism ; Viral Proteins ; Zidovudine/analogs & derivatives/chemistry/metabolism

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Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

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Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism (1994)

M. R. Sawaya ; H. Pelletier ; A. Kumar ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 264(5167): 1930-5.

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Publication Date: 1994-06-24

Description: Structures of the 31-kilodalton catalytic domain of rat DNA polymerase beta (pol beta) and the whole 39-kilodalton enzyme were determined at 2.3 and 3.6 angstrom resolution, respectively. The 31-kilodalton domain is composed of fingers, palm, and thumb subdomains arranged to form a DNA binding channel reminiscent of the polymerase domains of the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, and bacteriophage T7 RNA polymerase. The amino-terminal 8-kilodalton domain is attached to the fingers subdomain by a flexible hinge. The two invariant aspartates found in all polymerase sequences and implicated in catalytic activity have the same geometric arrangement within structurally similar but topologically distinct palms, indicating that the polymerases have maintained, or possibly re-evolved, a common nucleotidyl transfer mechanism. The location of Mn2+ and deoxyadenosine triphosphate in pol beta confirms the role of the invariant aspartates in metal ion and deoxynucleoside triphosphate binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sawaya, M R -- Pelletier, H -- Kumar, A -- Wilson, S H -- Kraut, J -- CA17374/CA/NCI NIH HHS/ -- ES06839/ES/NIEHS NIH HHS/ -- GM10928/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jun 24;264(5167):1930-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego 92093-0317.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7516581" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Binding Sites ; Cloning, Molecular ; Crystallization ; Crystallography, X-Ray ; DNA/metabolism ; DNA Polymerase I/*chemistry/metabolism ; DNA-Directed RNA Polymerases/chemistry/metabolism ; Deoxyadenine Nucleotides/chemistry/metabolism ; Deoxycytosine Nucleotides/chemistry/metabolism ; Dideoxynucleotides ; HIV Reverse Transcriptase ; Protein Folding ; Protein Structure, Secondary ; RNA-Directed DNA Polymerase/chemistry/metabolism ; Rats ; Recombinant Proteins/chemistry ; Viral Proteins

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How do enzymes work? (1988)

J. Kraut

American Association for the Advancement of Science (AAAS)

In: Science. 242(4878): 533-40.

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Publication Date: 1988-10-28

Description: The principle of transition-state stabilization asserts that the occurrence of enzymic catalysis is equivalent to saying that an enzyme binds the transition state much more strongly than it binds the ground-state reactants. An outline of the origin and gradual acceptance of this idea is presented, and elementary transition-state theory is reviewed. It is pointed out that a misconception about the theory has led to oversimplification of the accepted expression relating catalysis and binding, and an amended expression is given. Some implications of the transition-state binding principle are then explored. The amended expression suggests that internal molecular dynamics may also play a role in enzymic catalysis. Although such effects probably do not make a major contribution, their magnitude is completely unknown. Two examples of recent advances due to application of the transition-state binding principle are reviewed, one pertaining to the zinc protease mechanism and the other to the generation of catalytic antibodies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kraut, J -- New York, N.Y. -- Science. 1988 Oct 28;242(4878):533-40.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of California, San Diego, La Jolla 92093.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3051385" target="_blank"〉PubMed〈/a〉

Keywords: *Catalysis ; Chemistry, Physical ; DNA Mutational Analysis ; Enzymes/*physiology ; Physicochemical Phenomena ; Protein Conformation ; Structure-Activity Relationship

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Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

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Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis (1986)

E. E. Howell ; J. E. Villafranca ; M. S. Warren ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 231(4742): 1123-8.

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Publication Date: 1986-03-07

Description: The crystal structures and enzymic properties of two mutant dihydrofolate reductases (Escherichia coli) were studied in order to clarify the functional role of an invariant carboxylic acid (aspartic acid at position 27) at the substrate binding site. One mutation, constructed by oligonucleotide-directed mutagenesis, replaces Asp27 with asparagine; the other is a primary-site revertant to Ser27. The only structural perturbations involve two internally bound water molecules. Both mutants have low but readily measurable activity, which increases rapidly with decreasing pH. The mutant enzymes were also characterized with respect to relative folate: dihydrofolate activities and kinetic deuterium isotope effects. It is concluded that Asp27 participates in protonation of the substrate but not in electrostatic stabilization of a positively charged, protonated transition state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Howell, E E -- Villafranca, J E -- Warren, M S -- Oatley, S J -- Kraut, J -- F32 GM09375/GM/NIGMS NIH HHS/ -- GM10928/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1986 Mar 7;231(4742):1123-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/3511529" target="_blank"〉PubMed〈/a〉

Keywords: *Aspartic Acid ; Crystallography ; Deuterium ; Escherichia coli ; Kinetics ; Methotrexate/metabolism ; Mutation ; Protein Binding ; Structure-Activity Relationship ; *Tetrahydrofolate Dehydrogenase

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Directed mutagenesis of dihydrofolate reductase (1983)

J. E. Villafranca ; E. E. Howell ; D. H. Voet ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 222(4625): 782-8.

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Publication Date: 1983-11-18

Description: Three mutations of the enzyme dihydrofolate reductase were constructed by oligonucleotide-directed mutagenesis of the cloned Escherichia coli gene. The mutations--at residue 27, aspartic acid replaced with asparagine; at residue 39, proline replaced with cysteine; and at residue 95, glycine replaced with alanine--were designed to answer questions about the relations between molecular structure and function that were raised by the x-ray crystal structures. Properties of the mutant proteins show that Asp-27 is important for catalysis and that perturbation of the local structure at a conserved cis peptide bond following Gly-95 abolishes activity. Substitution of cysteine for proline at residue 39 results in the appearance of new forms of the enzyme that correspond to various oxidation states of the cysteine. One of these forms probably represents a species cross-linked by an intrachain disulfide bridge between the cysteine at position 85 and the new cysteine at position 39.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Villafranca, J E -- Howell, E E -- Voet, D H -- Strobel, M S -- Ogden, R C -- Abelson, J N -- Kraut, J -- CA17374/CA/NCI NIH HHS/ -- F32 GM09375/GM/NIGMS NIH HHS/ -- GM10928/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1983 Nov 18;222(4625):782-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/6356360" target="_blank"〉PubMed〈/a〉

Keywords: Amino Acid Sequence ; Base Sequence ; Disulfides ; Escherichia coli/genetics ; Gene Expression Regulation ; Genes ; Genes, Bacterial ; *Mutation ; Structure-Activity Relationship ; Tetrahydrofolate Dehydrogenase/*genetics

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Electronic ISSN: 1095-9203

Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics

Published by American Association for the Advancement of Science (AAAS)

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