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  1. Article: Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate.

    Borar, Prateeka / Biswas, Tapan / Chaudhuri, Ankur / Huxford, Tom / Chakrabarti, Saikat / Ghosh, Gourisankar / Polley, Smarajit

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Rapid and high-fidelity phosphorylation of two serines (S32 and S36) of IκBα by a prototype Ser/Thr kinase IKK2 is critical for fruitful canonical NF-κB activation. Here, we report that IKK2 is a dual specificity Ser/Thr kinase that autophosphorylates ... ...

    Abstract Rapid and high-fidelity phosphorylation of two serines (S32 and S36) of IκBα by a prototype Ser/Thr kinase IKK2 is critical for fruitful canonical NF-κB activation. Here, we report that IKK2 is a dual specificity Ser/Thr kinase that autophosphorylates itself at tyrosine residues in addition to its activation loop serines. Mutation of one such tyrosine, Y169, located in proximity to the active site, to phenylalanine, renders IKK2 inactive for phosphorylation of S32 of IκBα. Surprisingly, auto-phosphorylated IKK2 relayed phosphate group(s) to IκBα without ATP when ADP is present. We also observed that mutation of K44, an ATP-binding lysine conserved in all protein kinases, to methionine renders IKK2 inactive towards specific phosphorylation of S32 or S36 of IκBα, but not non-specific substrates. These observations highlight an unusual evolution of IKK2, in which autophosphorylation of tyrosine(s) in the activation loop and the invariant ATP-binding K44 residue define its signal-responsive substrate specificity ensuring the fidelity of NF-κB activation.
    Language English
    Publishing date 2024-03-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.06.27.546692
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Designing active RNF4 monomers by introducing a tryptophan: avidity towards E2∼Ub conjugates dictates the activity of ubiquitin RING E3 ligases.

    Sarkar, Sayani / Behera, Adaitya Prasad / Borar, Prateeka / Banka, Prerana Agarwal / Datta, Ajit B

    The Biochemical journal

    2019  Volume 476, Issue 10, Page(s) 1465–1482

    Abstract: Ubiquitin RING E3 ligases (E3s) catalyze ubiquitin (Ub) transfer to their substrates by engaging E2∼Ub intermediates with the help of their RING domains. Different E3s have been found to contain a conserved tryptophan residue in their RING that plays an ... ...

    Abstract Ubiquitin RING E3 ligases (E3s) catalyze ubiquitin (Ub) transfer to their substrates by engaging E2∼Ub intermediates with the help of their RING domains. Different E3s have been found to contain a conserved tryptophan residue in their RING that plays an essential role in E2 binding and, hence, enzymatic activity. Many active E3s, however, lack this specific residue. We mined through the existing data to observe that the conservation of the tryptophan and quaternary organization of the RING domains are remarkably correlated. Monomeric RINGs possess the tryptophan while all well-characterized dimeric RINGs, except RNF8, contain other amino acid residues. Biochemical analyses on representative E3s and their mutants reveal that the tryptophan is essential for optimal enzymatic activity of monomeric RINGs whereas dimeric E3s with tryptophan display hyperactivity. Most critically, the introduction of the tryptophan restores the activity of inactive monomeric RNF4 mutants, an obligatory dimeric E3. Binding studies indicate that monomeric RINGs retained the tryptophan for their optimal functionality to compensate for weak Ub binding. On the other hand, tryptophan was omitted from dimeric RINGs during the course of evolution to prevent unwanted modifications and allow regulation of their activity through oligomerization.
    MeSH term(s) Humans ; Mutation ; Nuclear Proteins/chemistry ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Protein Binding ; Protein Multimerization ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Tryptophan/chemistry ; Tryptophan/genetics ; Tryptophan/metabolism ; Ubiquitin/chemistry ; Ubiquitin/genetics ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/chemistry ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism
    Chemical Substances Nuclear Proteins ; RNF4 protein, human ; Transcription Factors ; Ubiquitin ; Tryptophan (8DUH1N11BX) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Language English
    Publishing date 2019-05-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2969-5
    ISSN 1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
    ISSN (online) 1470-8728
    ISSN 0006-2936 ; 0306-3275 ; 0264-6021
    DOI 10.1042/BCJ20180883
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Correction: Designing active RNF4 monomers by introducing a tryptophan: avidity towards E2∼Ub conjugates dictates the activity of ubiquitin RING E3 ligases.

    Sarkar, Sayani / Behera, Adaitya Prasad / Borar, Prateeka / Banka, Prerana Agarwal / Datta, Ajit B

    The Biochemical journal

    2019  Volume 476, Issue 17, Page(s) 2517–2518

    Language English
    Publishing date 2019-09-13
    Publishing country England
    Document type Journal Article ; Published Erratum
    ZDB-ID 2969-5
    ISSN 1470-8728 ; 0006-2936 ; 0306-3275 ; 0264-6021
    ISSN (online) 1470-8728
    ISSN 0006-2936 ; 0306-3275 ; 0264-6021
    DOI 10.1042/BCJ20180883_COR
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Identification of Biomarker Hyaluronan on Colon Cancer Extracellular Vesicles Using Correlative AFM and Spectroscopy.

    Paul, Debashish / Roy, Anuradha / Nandy, Arpita / Datta, Brateen / Borar, Prateeka / Pal, Samir Kumar / Senapati, Dulal / Rakshit, Tatini

    The journal of physical chemistry letters

    2020  Volume 11, Issue 14, Page(s) 5569–5576

    Abstract: Extracellular vesicles (EVs), naturally occurring nanosized vesicles secreted from cells, are essential for intercellular communication. They carry unique biomolecules on the surface or interior that are of great interest as biomarkers for various ... ...

    Abstract Extracellular vesicles (EVs), naturally occurring nanosized vesicles secreted from cells, are essential for intercellular communication. They carry unique biomolecules on the surface or interior that are of great interest as biomarkers for various pathological conditions such as cancer. In this work, we use high-resolution atomic force microscopy (AFM) and spectroscopy (AFS) techniques to demonstrate differences between EVs derived from colon cancer cells and colon epithelial cells at the single-vesicle level. We observe that EV populations are significantly increased in the cancer cell media compared to the normal cell EVs. We show that both EVs display an EV marker, CD9, while EVs derived from the cancer cells are slightly higher in density. Hyaluronan (HA) is a nonsulfated glycosaminoglycan linked to malignant tumor growth according to recent reports. Interestingly, at the single-vesicle level, colon cancer EVs exhibit significantly increased HA surface densities compared to the normal EVs. Spectroscopic measurements such as Fourier transform infrared (FT-IR), circular dichroism (CD), and Raman spectroscopy unequivocally support the AFM and AFS measurements. To our knowledge, it represents the first report of detecting HA-coated EVs as a potential colon cancer biomarker. Taken together, this sensitive approach will be useful in identifying biomarkers in the early stages of detection and evaluation of cancer.
    MeSH term(s) Biomarkers, Tumor/analysis ; Biomarkers, Tumor/metabolism ; Cell Line, Tumor ; Colonic Neoplasms/metabolism ; Colonic Neoplasms/pathology ; Epithelial Cells/metabolism ; Extracellular Vesicles/metabolism ; Humans ; Hyaluronic Acid/analysis ; Hyaluronic Acid/metabolism ; Microscopy, Atomic Force ; Spectrophotometry, Atomic ; Tetraspanin 29/analysis
    Chemical Substances Biomarkers, Tumor ; CD9 protein, human ; Tetraspanin 29 ; Hyaluronic Acid (9004-61-9)
    Language English
    Publishing date 2020-06-30
    Publishing country United States
    Document type Journal Article
    ISSN 1948-7185
    ISSN (online) 1948-7185
    DOI 10.1021/acs.jpclett.0c01018
    Database MEDical Literature Analysis and Retrieval System OnLINE

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