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  1. Article ; Online: Structural basis for the role of C-terminus acidic tail of Saccharomyces cerevisiae ubiquitin-conjugating enzyme (Rad6) in E3 ligase (Bre1) mediated recognition of histones.

    Yadav, Pawan / Gupta, Manish / Wazahat, Rushna / Islam, Zeyaul / Tsutakawa, Susan E / Kamthan, Mohan / Kumar, Pankaj

    International journal of biological macromolecules

    2023  Volume 254, Issue Pt 2, Page(s) 127717

    Abstract: Ubiquitination of histone H2B on chromatin is key to gene regulation. E3 ligase Bre1 and E2 Rad6 in Saccharomyces cerevisiae associate together to catalyze mono-ubiquitination at histone ... ...

    Abstract Ubiquitination of histone H2B on chromatin is key to gene regulation. E3 ligase Bre1 and E2 Rad6 in Saccharomyces cerevisiae associate together to catalyze mono-ubiquitination at histone H2B
    MeSH term(s) Histones/genetics ; Ubiquitin-Conjugating Enzymes/genetics ; Ubiquitin-Conjugating Enzymes/metabolism ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Ubiquitin-Protein Ligases/genetics ; Scattering, Small Angle ; Saccharomyces cerevisiae Proteins/chemistry ; X-Ray Diffraction
    Chemical Substances Histones ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Saccharomyces cerevisiae Proteins ; Bre1 protein, S cerevisiae
    Language English
    Publishing date 2023-11-02
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2023.127717
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    In stock of ZB MED Cologne/Königswinter

    Zs.B 2374: Show issues Location:
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  2. Article: The NS1 protein of influenza B virus binds 5'-triphosphorylated dsRNA to suppress RIG-I activation and the host antiviral response.

    Woltz, Ryan / Schweibenz, Brandon / Tsutakawa, Susan E / Zhao, Chen / Ma, LiChung / Shurina, Ben / Hura, Gregory L / John, Rachael / Vorobiev, Sergey / Swapna, Gvt / Solotchi, Mihai / Tainer, John A / Krug, Robert M / Patel, Smita S / Montelione, Gaetano T

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Influenza A and B viruses overcome the host antiviral response to cause a contagious and often severe human respiratory disease. Here, integrative structural biology and biochemistry studies on non-structural protein 1 of influenza B virus (NS1B) reveal ... ...

    Abstract Influenza A and B viruses overcome the host antiviral response to cause a contagious and often severe human respiratory disease. Here, integrative structural biology and biochemistry studies on non-structural protein 1 of influenza B virus (NS1B) reveal a previously unrecognized viral mechanism for innate immune evasion. Conserved basic groups of its C-terminal domain (NS1B-CTD) bind 5'triphosphorylated double-stranded RNA (5'-ppp-dsRNA), the primary pathogen-associated feature that activates the host retinoic acid-inducible gene I protein (RIG-I) to initiate interferon synthesis and the cellular antiviral response. Like RIG-I, NS1B-CTD preferentially binds blunt-end 5'ppp-dsRNA. NS1B-CTD also competes with RIG-I for binding 5'ppp-dsRNA, and thus suppresses activation of RIG-I's ATPase activity. Although the NS1B N-terminal domain also binds dsRNA, it utilizes a different binding mode and lacks 5'ppp-dsRNA end preferences. In cells infected with wild-type influenza B virus, RIG-I activation is inhibited. In contrast, RIG-I activation and the resulting phosphorylation of transcription factor IRF-3 are not inhibited in cells infected with a mutant virus encoding NS1B with a R208A substitution it its CTD that eliminates its 5'ppp-dsRNA binding activity. These results reveal a novel mechanism in which NS1B binds 5'ppp-dsRNA to inhibit the RIG-I antiviral response during influenza B virus infection, and open the door to new avenues for antiviral drug discovery.
    Language English
    Publishing date 2024-01-24
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.09.25.559316
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  3. Article ; Online: Conformational Dynamics in the Interaction of SARS-CoV-2 Papain-like Protease with Human Interferon-Stimulated Gene 15 Protein.

    Leite, Wellington C / Weiss, Kevin L / Phillips, Gwyndalyn / Zhang, Qiu / Qian, Shuo / Tsutakawa, Susan E / Coates, Leighton / O'Neill, Hugh

    The journal of physical chemistry letters

    2021  Volume 12, Issue 23, Page(s) 5608–5615

    Abstract: Papain-like protease (PLpro) from SARS-CoV-2 plays essential roles in the replication cycle of the virus. In particular, it preferentially interacts with and cleaves human interferon-stimulated gene 15 (hISG15) to suppress the innate immune response of ... ...

    Abstract Papain-like protease (PLpro) from SARS-CoV-2 plays essential roles in the replication cycle of the virus. In particular, it preferentially interacts with and cleaves human interferon-stimulated gene 15 (hISG15) to suppress the innate immune response of the host. We used small-angle X-ray and neutron scattering combined with computational techniques to study the mechanism of interaction of SARS-CoV-2 PLpro with hISG15. We showed that hISG15 undergoes a transition from an extended to a compact state after binding to PLpro, a conformation that has not been previously observed in complexes of SARS-CoV-2 PLpro with ISG15 from other species. Furthermore, computational analysis showed significant conformational flexibility in the ISG15 N-terminal domain, suggesting that it is weakly bound to PLpro and supports a binding mechanism that is dominated by the C-terminal ISG15 domain. This study fundamentally improves our understanding of the SARS-CoV-2 deISGylation complex that will help guide development of COVID-19 therapeutics targeting this complex.
    MeSH term(s) Coronavirus Papain-Like Proteases/chemistry ; Coronavirus Papain-Like Proteases/genetics ; Coronavirus Papain-Like Proteases/metabolism ; Cytokines/chemistry ; Cytokines/genetics ; Cytokines/metabolism ; Humans ; Interferons/metabolism ; Neutron Diffraction ; Protein Conformation ; SARS-CoV-2/enzymology ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Scattering, Small Angle ; Ubiquitins/chemistry ; Ubiquitins/genetics ; Ubiquitins/metabolism ; X-Ray Diffraction
    Chemical Substances Cytokines ; Ubiquitins ; ISG15 protein, human (60267-61-0) ; Interferons (9008-11-1) ; Coronavirus Papain-Like Proteases (EC 3.4.22.2) ; papain-like protease, SARS-CoV-2 (EC 3.4.22.2)
    Language English
    Publishing date 2021-06-10
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.1c00831
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  4. Article ; Online: The Role of XPB/Ssl2 dsDNA Translocase Processivity in Transcription Start-site Scanning.

    Tomko, Eric J / Luyties, Olivia / Rimel, Jenna K / Tsai, Chi-Lin / Fuss, Jill O / Fishburn, James / Hahn, Steven / Tsutakawa, Susan E / Taatjes, Dylan J / Galburt, Eric A

    Journal of molecular biology

    2021  Volume 433, Issue 14, Page(s) 166813

    Abstract: ... complexes (i.e. seven subunits, lacking the kinase module) from both S. cerevisiae and H. sapiens. We find ... productive start-sites. The ten-subunit holo-TFIIH from S. cerevisiae has a processive dsDNA translocase ... scanning in humans. Furthermore, in contrast to holo-TFIIH, the S. cerevisiae core-TFIIH also lacks ...

    Abstract The general transcription factor TFIIH contains three ATP-dependent catalytic activities. TFIIH functions in nucleotide excision repair primarily as a DNA helicase and in Pol II transcription initiation as a dsDNA translocase and protein kinase. During initiation, the XPB/Ssl2 subunit of TFIIH couples ATP hydrolysis to dsDNA translocation facilitating promoter opening and the kinase module phosphorylates Pol II to facilitate the transition to elongation. These functions are conserved between metazoans and yeast; however, yeast TFIIH also drives transcription start-site scanning in which Pol II scans downstream DNA to locate productive start-sites. The ten-subunit holo-TFIIH from S. cerevisiae has a processive dsDNA translocase activity required for scanning and a structural role in scanning has been ascribed to the three-subunit TFIIH kinase module. Here, we assess the dsDNA translocase activity of ten-subunit holo- and core-TFIIH complexes (i.e. seven subunits, lacking the kinase module) from both S. cerevisiae and H. sapiens. We find that neither holo nor core human TFIIH exhibit processive translocation, consistent with the lack of start-site scanning in humans. Furthermore, in contrast to holo-TFIIH, the S. cerevisiae core-TFIIH also lacks processive translocation and its dsDNA-stimulated ATPase activity was reduced ~5-fold to a level comparable to the human complexes, potentially explaining the reported upstream shift in start-site observed in vitro in the absence of the S. cerevisiae kinase module. These results suggest that neither human nor S. cerevisiae core-TFIIH can translocate efficiently, and that the S. cerevisiae kinase module functions as a processivity factor to allow for robust transcription start-site scanning.
    MeSH term(s) Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; DNA/genetics ; DNA/metabolism ; DNA Helicases/metabolism ; DNA-Binding Proteins/metabolism ; Gene Expression Regulation ; Humans ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Transcription Factor TFIIH/metabolism ; Transcription Initiation Site ; Transcription Initiation, Genetic
    Chemical Substances DNA-Binding Proteins ; XPBC-ERCC-3 protein (146045-44-5) ; Transcription Factor TFIIH (148710-81-0) ; Adenosine Triphosphate (8L70Q75FXE) ; DNA (9007-49-2) ; Adenosine Triphosphatases (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-)
    Language English
    Publishing date 2021-01-13
    Publishing country Netherlands
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2021.166813
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    Zs.A 867: Show issues Location:
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  5. Article: Bending Forks and Wagging Dogs—It’s about the DNA 3′ Tail

    Tsutakawa, Susan E / John A. Tainer

    Molecular cell. 2015 June 18, v. 58

    2015  

    Abstract: ... find that unexpected HLTF specificity for DNA’s 3′-hydroxyl tail helps control these biological ...

    Abstract Protecting, reversing, and remodeling stalled replication forks are critical to genome stability and require coordinating DNA replication, remodeling, and repair. In this issue, Kile et al. (2015) find that unexpected HLTF specificity for DNA’s 3′-hydroxyl tail helps control these biological functions.
    Keywords DNA ; DNA repair ; DNA replication ; genome
    Language English
    Dates of publication 2015-0618
    Size p. 972-973.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2015.06.005
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  6. Article ; Online: EXO5-DNA structure and BLM interactions direct DNA resection critical for ATR-dependent replication restart.

    Hambarde, Shashank / Tsai, Chi-Lin / Pandita, Raj K / Bacolla, Albino / Maitra, Anirban / Charaka, Vijay / Hunt, Clayton R / Kumar, Rakesh / Limbo, Oliver / Le Meur, Remy / Chazin, Walter J / Tsutakawa, Susan E / Russell, Paul / Schlacher, Katharina / Pandita, Tej K / Tainer, John A

    Molecular cell

    2021  Volume 81, Issue 14, Page(s) 2989–3006.e9

    Abstract: Stalled DNA replication fork restart after stress as orchestrated by ATR kinase, BLM helicase, and structure-specific nucleases enables replication, cell survival, and genome stability. Here we unveil human exonuclease V (EXO5) as an ATR-regulated DNA ... ...

    Abstract Stalled DNA replication fork restart after stress as orchestrated by ATR kinase, BLM helicase, and structure-specific nucleases enables replication, cell survival, and genome stability. Here we unveil human exonuclease V (EXO5) as an ATR-regulated DNA structure-specific nuclease and BLM partner for replication fork restart. We find that elevated EXO5 in tumors correlates with increased mutation loads and poor patient survival, suggesting that EXO5 upregulation has oncogenic potential. Structural, mechanistic, and mutational analyses of EXO5 and EXO5-DNA complexes reveal a single-stranded DNA binding channel with an adjacent ATR phosphorylation motif (T88Q89) that regulates EXO5 nuclease activity and BLM binding identified by mass spectrometric analysis. EXO5 phospho-mimetic mutant rescues the restart defect from EXO5 depletion that decreases fork progression, DNA damage repair, and cell survival. EXO5 depletion furthermore rescues survival of FANCA-deficient cells and indicates EXO5 functions epistatically with SMARCAL1 and BLM. Thus, an EXO5 axis connects ATR and BLM in directing replication fork restart.
    MeSH term(s) Ataxia Telangiectasia Mutated Proteins/genetics ; Cell Line ; Cell Line, Tumor ; DNA/genetics ; DNA Damage/genetics ; DNA Helicases/genetics ; DNA Mutational Analysis/methods ; DNA Repair/genetics ; DNA Replication/genetics ; DNA-Binding Proteins/genetics ; Exonucleases/genetics ; Genomic Instability/genetics ; HEK293 Cells ; HeLa Cells ; Humans ; Mutation/genetics ; Oncogenes/genetics ; Phosphorylation/genetics ; RecQ Helicases/genetics ; Up-Regulation/genetics
    Chemical Substances DNA-Binding Proteins ; DNA (9007-49-2) ; ATR protein, human (EC 2.7.11.1) ; Ataxia Telangiectasia Mutated Proteins (EC 2.7.11.1) ; EXO5 protein, human (EC 3.1.-) ; Exonucleases (EC 3.1.-) ; Bloom syndrome protein (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-) ; RecQ Helicases (EC 3.6.4.12)
    Language English
    Publishing date 2021-06-30
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2021.05.027
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    Zs.A 5055: Show issues Location:
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  7. Article ; Online: Small angle X-ray scattering-assisted protein structure prediction in CASP13 and emergence of solution structure differences.

    Hura, Greg L / Hodge, Curtis D / Rosenberg, Daniel / Guzenko, Dmytro / Duarte, Jose M / Monastyrskyy, Bohdan / Grudinin, Sergei / Kryshtafovych, Andriy / Tainer, John A / Fidelis, Krzysztof / Tsutakawa, Susan E

    Proteins

    2019  Volume 87, Issue 12, Page(s) 1298–1314

    Abstract: ... that these proteins adopt different conformation(s) in solution. This CASP13 result, if representative of PDB ...

    Abstract Small angle X-ray scattering (SAXS) measures comprehensive distance information on a protein's structure, which can constrain and guide computational structure prediction algorithms. Here, we evaluate structure predictions of 11 monomeric and oligomeric proteins for which SAXS data were collected and provided to predictors in the 13th round of the Critical Assessment of protein Structure Prediction (CASP13). The category for SAXS-assisted predictions made gains in certain areas for CASP13 compared to CASP12. Improvements included higher quality data with size exclusion chromatography-SAXS (SEC-SAXS) and better selection of targets and communication of results by CASP organizers. In several cases, we can track improvements in model accuracy with use of SAXS data. For hard multimeric targets where regular folding algorithms were unsuccessful, SAXS data helped predictors to build models better resembling the global shape of the target. For most models, however, no significant improvement in model accuracy at the domain level was registered from use of SAXS data, when rigorously comparing SAXS-assisted models to the best regular server predictions. To promote future progress in this category, we identify successes, challenges, and opportunities for improved strategies in prediction, assessment, and communication of SAXS data to predictors. An important observation is that, for many targets, SAXS data were inconsistent with crystal structures, suggesting that these proteins adopt different conformation(s) in solution. This CASP13 result, if representative of PDB structures and future CASP targets, may have substantive implications for the structure training databases used for machine learning, CASP, and use of prediction models for biology.
    MeSH term(s) Algorithms ; Computational Biology ; Models, Molecular ; Protein Conformation ; Protein Folding ; Proteins/chemistry ; Proteins/genetics ; Proteins/ultrastructure ; Scattering, Small Angle ; Solutions/chemistry ; X-Ray Diffraction
    Chemical Substances Proteins ; Solutions
    Language English
    Publishing date 2019-10-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 806683-8
    ISSN 1097-0134 ; 0887-3585
    ISSN (online) 1097-0134
    ISSN 0887-3585
    DOI 10.1002/prot.25827
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    Zs.A 2291: Show issues Location:
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  8. 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
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  9. 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
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  10. Article ; Online: Dissection of DNA double-strand-break repair using novel single-molecule forceps.

    Wang, Jing L / Duboc, Camille / Wu, Qian / Ochi, Takashi / Liang, Shikang / Tsutakawa, Susan E / Lees-Miller, Susan P / Nadal, Marc / Tainer, John A / Blundell, Tom L / Strick, Terence R

    Nature structural & molecular biology

    2018  Volume 25, Issue 6, Page(s) 482–487

    Abstract: ... DNA end synapsis on the 100 ms timescale, and the addition of PAXX extends this lifetime to ~2 s ...

    Abstract Repairing DNA double-strand breaks (DSBs) by nonhomologous end joining (NHEJ) requires multiple proteins to recognize and bind DNA ends, process them for compatibility, and ligate them together. We constructed novel DNA substrates for single-molecule nanomanipulation, allowing us to mechanically detect, probe, and rupture in real-time DSB synapsis by specific human NHEJ components. DNA-PKcs and Ku allow DNA end synapsis on the 100 ms timescale, and the addition of PAXX extends this lifetime to ~2 s. Further addition of XRCC4, XLF and ligase IV results in minute-scale synapsis and leads to robust repair of both strands of the nanomanipulated DNA. The energetic contribution of the different components to synaptic stability is typically on the scale of a few kilocalories per mole. Our results define assembly rules for NHEJ machinery and unveil the importance of weak interactions, rapidly ruptured even at sub-picoNewton forces, in regulating this multicomponent chemomechanical system for genome integrity.
    MeSH term(s) Animals ; Calcium-Binding Proteins/metabolism ; Chromosome Pairing ; DNA/genetics ; DNA/metabolism ; DNA Breaks, Double-Stranded ; DNA End-Joining Repair ; DNA Ligase ATP/metabolism ; DNA Repair Enzymes/metabolism ; DNA Restriction Enzymes/metabolism ; DNA-Binding Proteins/metabolism ; Genetic Techniques/instrumentation ; Humans ; Ku Autoantigen/metabolism ; Phosphorylation ; Sf9 Cells ; Spodoptera
    Chemical Substances CIB1 protein, human ; Calcium-Binding Proteins ; DNA-Binding Proteins ; NHEJ1 protein, human ; PAXX protein, human ; XRCC4 protein, human ; DNA (9007-49-2) ; DNA Restriction Enzymes (EC 3.1.21.-) ; XRCC5 protein, human (EC 3.6.4.12) ; Ku Autoantigen (EC 4.2.99.-) ; DNA Repair Enzymes (EC 6.5.1.-) ; DNA Ligase ATP (EC 6.5.1.1)
    Language English
    Publishing date 2018-05-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-018-0065-1
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