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  1. Article: New recognition mode for a TG mismatch: the atomic structure of a very short patch repair endonuclease-DNA complex.

    Tsutakawa, S E / Morikawa, K

    Cold Spring Harbor symposia on quantitative biology

    2003  Volume 65, Page(s) 233–239

    MeSH term(s) Base Pair Mismatch/genetics ; DNA/genetics ; DNA/metabolism ; DNA Damage/genetics ; DNA Repair/genetics ; Endodeoxyribonucleases/genetics ; Endodeoxyribonucleases/metabolism ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Guanine ; Thymine
    Chemical Substances Guanine (5Z93L87A1R) ; DNA (9007-49-2) ; Endodeoxyribonucleases (EC 3.1.-) ; vsr endonuclease (EC 3.1.21.-) ; Thymine (QR26YLT7LT)
    Language English
    Publishing date 2003-05-11
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 0091-7451
    ISSN 0091-7451
    DOI 10.1101/sqb.2000.65.233
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Transcription-coupled repair of oxidative DNA damage in human cells: mechanisms and consequences.

    Tsutakawa, S E / Cooper, P K

    Cold Spring Harbor symposia on quantitative biology

    2003  Volume 65, Page(s) 201–215

    MeSH term(s) Cockayne Syndrome/genetics ; DNA Damage/genetics ; DNA Repair/genetics ; DNA-Directed RNA Polymerases/genetics ; Humans ; Models, Genetic ; Transcription, Genetic ; Xeroderma Pigmentosum/genetics
    Chemical Substances DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2003-05-11
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S. ; Review
    ISSN 0091-7451
    ISSN 0091-7451
    DOI 10.1101/sqb.2000.65.201
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The structural basis of damaged DNA recognition and endonucleolytic cleavage for very short patch repair endonuclease.

    Tsutakawa, S E / Morikawa, K

    Nucleic acids research

    2001  Volume 29, Issue 18, Page(s) 3775–3783

    Abstract: Endonucleases in DNA repair must be able to recognize damaged DNA as well as cleave the phosphodiester backbone. These functional prerequisites are manifested in very short patch repair (Vsr) endonuclease through a common endonuclease topology that has ... ...

    Abstract Endonucleases in DNA repair must be able to recognize damaged DNA as well as cleave the phosphodiester backbone. These functional prerequisites are manifested in very short patch repair (Vsr) endonuclease through a common endonuclease topology that has been tailored for recognition of TG mismatches. Structural and biochemical comparison with type II restriction enzymes illustrates how Vsr resembles these endonucleases in overall topology but also how Vsr diverges in terms of the detailed catalytic mechanism. A histidine and two metal-water clusters catalyze the phosphodiester cleavage. The mode of DNA damage recognition is also unique to Vsr. All other structurally characterized DNA damage-binding enzymes employ a nucleotide flipping mechanism for substrate recognition and for catalysis. Vsr, on the other hand, recognizes the TG mismatch as a wobble base pair and penetrates the DNA with three aromatic residues on one side of the mismatch. Thus, Vsr endonuclease provides important counterpoints in our understanding of endonucleolytic mechanisms and of damaged DNA recognition.
    MeSH term(s) Catalysis ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Damage ; DNA Repair ; Endodeoxyribonucleases/chemistry ; Endodeoxyribonucleases/metabolism ; Nucleic Acid Conformation ; Protein Conformation
    Chemical Substances DNA (9007-49-2) ; Endodeoxyribonucleases (EC 3.1.-) ; vsr endonuclease (EC 3.1.21.-)
    Language English
    Publishing date 2001-02-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/29.18.3775
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The structural basis for the functional comparability of factor VIII and the long-acting variant recombinant factor VIII Fc fusion protein.

    Leksa, N C / Chiu, P-L / Bou-Assaf, G M / Quan, C / Liu, Z / Goodman, A B / Chambers, M G / Tsutakawa, S E / Hammel, M / Peters, R T / Walz, T / Kulman, J D

    Journal of thrombosis and haemostasis : JTH

    2017  Volume 15, Issue 6, Page(s) 1167–1179

    Abstract: Essentials Recombinant factor VIII (rFVIII) Fc fusion protein has a 1.5-fold longer half-life than rFVIII. Five orthogonal methods were used to characterize the structure of rFVIIIFc compared to rFVIII. The C-terminal Fc fusion does not perturb the ... ...

    Abstract Essentials Recombinant factor VIII (rFVIII) Fc fusion protein has a 1.5-fold longer half-life than rFVIII. Five orthogonal methods were used to characterize the structure of rFVIIIFc compared to rFVIII. The C-terminal Fc fusion does not perturb the structure of FVIII in rFVIIIFc. The FVIII and Fc components of rFVIIIFc are flexibly tethered and functionally independent.
    Summary: Background Fusion of the human IgG
    MeSH term(s) Crystallography, X-Ray ; Factor VIII/administration & dosage ; Factor VIII/chemistry ; HEK293 Cells ; Half-Life ; Hemophilia A/drug therapy ; Hemophilia A/immunology ; Hemorrhage ; Humans ; Immunoglobulin Fc Fragments/administration & dosage ; Immunoglobulin Fc Fragments/chemistry ; Kinetics ; Mass Spectrometry ; Microscopy, Electron ; Peptide Fragments/chemistry ; Protein Domains ; Recombinant Fusion Proteins/administration & dosage ; Recombinant Fusion Proteins/chemistry ; Scattering, Small Angle ; Surface Plasmon Resonance ; X-Ray Diffraction
    Chemical Substances B-domain-deleted factor VIII ; Immunoglobulin Fc Fragments ; Peptide Fragments ; Recombinant Fusion Proteins ; factor VIII-Fc fusion protein ; F8 protein, human (839MOZ74GK) ; Factor VIII (9001-27-8)
    Language English
    Publishing date 2017-05-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 2112661-6
    ISSN 1538-7836 ; 1538-7933
    ISSN (online) 1538-7836
    ISSN 1538-7933
    DOI 10.1111/jth.13700
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  5. Article: Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex.

    Tsutakawa, S E / Jingami, H / Morikawa, K

    Cell

    1999  Volume 99, Issue 6, Page(s) 615–623

    Abstract: The crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution. In E. coli, the enzyme recognizes a TG mismatched base pair, generated after ... ...

    Abstract The crystal structure of very short patch repair (Vsr) endonuclease, in complex with Mg2+ and with duplex DNA containing a TG mismatch, has been determined at 2.3 A resolution. In E. coli, the enzyme recognizes a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine. Extensive interactions between the DNA and the protein characterize a novel recognition mechanism, where three aromatic residues intercalate from the major groove into the DNA to strikingly deform the base pair stacking. With the presence of a cleaved DNA intermediate in the active center, the structure of the Vsr/DNA complex provides detailed insights into the catalytic mechanism for endonuclease activity.
    MeSH term(s) Base Pair Mismatch ; Catalytic Domain ; Crystallography ; DNA/chemistry ; DNA Repair ; Deoxyribonuclease I/chemistry ; Escherichia coli/chemistry ; Magnesium/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Secondary ; Water/chemistry
    Chemical Substances Water (059QF0KO0R) ; DNA (9007-49-2) ; Deoxyribonuclease I (EC 3.1.21.1) ; Magnesium (I38ZP9992A)
    Language English
    Publishing date 1999-12-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/s0092-8674(00)81550-0
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  6. Article: Determination of in vivo phosphorylation sites in protein kinase C.

    Tsutakawa, S E / Medzihradszky, K F / Flint, A J / Burlingame, A L / Koshland, D E

    The Journal of biological chemistry

    1995  Volume 270, Issue 45, Page(s) 26807–26812

    Abstract: The primary structure of rat protein kinase C beta II was probed by high pressure liquid chromatography directly coupled to an electrospray ionization mass spectrometer and by high energy collision-induced dissociation analysis to identify in vivo ... ...

    Abstract The primary structure of rat protein kinase C beta II was probed by high pressure liquid chromatography directly coupled to an electrospray ionization mass spectrometer and by high energy collision-induced dissociation analysis to identify in vivo phosphorylation sites. The N-terminal methionine was found to be cleaved post-translationally and replaced with an acetyl group. Four phosphopeptides were identified. Two peptides, Thr500-Lys520 and Glu490-Lys520, are phosphorylated at Thr500 greater than 90%. Peptide His636-Arg649 is phosphorylated about 75% at Thr641. It is the only site that was previously identified during the in vitro autophosphorylation studies (Flint, A.J., Paladini, R.D., and Koshland, D.E., Jr. (1990) Science 249, 408-411). The fourth peptide Asn650-Lys672 is phosphorylated at Thr660. A discussion of the potential implication of these results follows.
    MeSH term(s) Amino Acid Sequence ; Animals ; Binding Sites ; Enzyme Activation ; Mass Spectrometry ; Molecular Sequence Data ; Molecular Structure ; Peptide Fragments/chemistry ; Peptide Fragments/genetics ; Peptide Fragments/metabolism ; Phosphorylation ; Protein Kinase C/chemistry ; Protein Kinase C/genetics ; Protein Kinase C/metabolism ; Protein Processing, Post-Translational ; Rats ; Sequence Homology, Amino Acid
    Chemical Substances Peptide Fragments ; Protein Kinase C (EC 2.7.11.13)
    Language English
    Publishing date 1995-11-10
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1074/jbc.270.45.26807
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    Uc I Zs.108: Show issues Location:
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  7. Article: Crystallographic and functional studies of very short patch repair endonuclease.

    Tsutakawa, S E / Muto, T / Kawate, T / Jingami, H / Kunishima, N / Ariyoshi, M / Kohda, D / Nakagawa, M / Morikawa, K

    Molecular cell

    1999  Volume 3, Issue 5, Page(s) 621–628

    Abstract: Vsr endonuclease plays a crucial role in the repair of TG mismatched base pairs, which are generated by the spontaneous degradation of methylated cytidines; Vsr recognizes the mismatched base pair and cleaves the phosphate backbone 5' to the thymidine. ... ...

    Abstract Vsr endonuclease plays a crucial role in the repair of TG mismatched base pairs, which are generated by the spontaneous degradation of methylated cytidines; Vsr recognizes the mismatched base pair and cleaves the phosphate backbone 5' to the thymidine. We have determined the crystal structure of a truncated form of this endonuclease at 1.8 A resolution. The protein contains one structural zinc-binding module. Unexpectedly, its overall topology resembles members of the type II restriction endonuclease family. Subsequent mutational and biochemical analyses showed that certain elements in the catalytic site are also conserved. However, the identification of a critical histidine and evidence of an active site metal-binding coordination that is novel to endonucleases indicate a distinct catalytic mechanism.
    MeSH term(s) Alanine ; Base Pair Mismatch ; Catalytic Domain ; Conserved Sequence ; Crystallography ; DNA Repair ; Deoxyribonucleases, Type II Site-Specific/chemistry ; Deoxyribonucleases, Type II Site-Specific/genetics ; Deoxyribonucleases, Type II Site-Specific/metabolism ; Endodeoxyribonucleases/chemistry ; Endodeoxyribonucleases/genetics ; Endodeoxyribonucleases/metabolism ; Manganese/metabolism ; Molecular Sequence Data ; Mutagenesis ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid ; Static Electricity
    Chemical Substances Manganese (42Z2K6ZL8P) ; Endodeoxyribonucleases (EC 3.1.-) ; vsr endonuclease (EC 3.1.21.-) ; Deoxyribonucleases, Type II Site-Specific (EC 3.1.21.4) ; Alanine (OF5P57N2ZX)
    Language English
    Publishing date 1999-05
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/s1097-2765(00)80355-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 5055: Show issues Location:
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  8. Article: Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting.

    Finer-Moore, J / Tsutakawa, S E / Cherbavaz, D R / LaPorte, D C / Koshland, D E / Stroud, R M

    Biochemistry

    1997  Volume 36, Issue 45, Page(s) 13890–13896

    Abstract: To clarify further the mechanism of regulation by phosphorylation of isocitrate dehydrogenase, cocrystallization of isocitrate dehydrogenase and isocitrate dehydrogenase kinase/phosphatase in the presence of an ATP analog was attempted. Although ... ...

    Abstract To clarify further the mechanism of regulation by phosphorylation of isocitrate dehydrogenase, cocrystallization of isocitrate dehydrogenase and isocitrate dehydrogenase kinase/phosphatase in the presence of an ATP analog was attempted. Although cocrystallization was unsuccessful, a new crystal form of isocitrate dehydrogenase was obtained which provides insight into the phosphorylation mechanism. The new, orthorhombic crystal form of isocitrate dehydrogenase is related to the previously reported tetragonal form largely by an approximately 16 degrees shift of a large domain relative to the small domain and clasp region within each subunit of the dimeric enzyme. The NADP+ cofactor binding surface is significantly disrupted by the shift to the open conformation. The solvent-accessible surface area and surface-enclosed volume increase by 2% relative to the dimeric tetragonal form. Most of the increase results from expansion of the active site cleft such that the distance across its opening increases from approximately 5 to 13 A, significantly increasing accessibility to Ser-113. The conformation of isocitrate dehydrogenase in the orthorhombic crystal form more closely resembles that of the crystal structure of the homologous enzyme 3-isopropylmalate dehydrogenase than does the tetragonal isocitrate dehydrogenase conformation. Since the crystal lattice forces are fairly weak, it appears that isocitrate dehydrogenase is a flexible molecule that can easily undergo domain shifts and possibly other induced fit conformational changes, to accommodate binding to isocitrate dehydrogenase kinase/phosphatase.
    MeSH term(s) Binding Sites ; Crystallization ; Crystallography, X-Ray ; Isocitrate Dehydrogenase/chemistry ; Isocitrate Dehydrogenase/metabolism ; Models, Molecular ; Phosphorylation ; Phosphoserine/metabolism ; Protein Conformation ; Protein Structure, Tertiary ; Substrate Specificity
    Chemical Substances Phosphoserine (17885-08-4) ; Isocitrate Dehydrogenase (EC 1.1.1.41)
    Language English
    Publishing date 1997-11-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/bi9711691
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