1
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Reinhardt R, Leonard TA. A critical evaluation of protein kinase regulation by activation loop autophosphorylation. eLife 2023; 12:e88210. [PMID: 37470698 PMCID: PMC10359097 DOI: 10.7554/elife.88210] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023] Open
Abstract
Phosphorylation of proteins is a ubiquitous mechanism of regulating their function, localization, or activity. Protein kinases, enzymes that use ATP to phosphorylate protein substrates are, therefore, powerful signal transducers in eukaryotic cells. The mechanism of phosphoryl-transfer is universally conserved among protein kinases, which necessitates the tight regulation of kinase activity for the orchestration of cellular processes with high spatial and temporal fidelity. In response to a stimulus, many kinases enhance their own activity by autophosphorylating a conserved amino acid in their activation loop, but precisely how this reaction is performed is controversial. Classically, kinases that autophosphorylate their activation loop are thought to perform the reaction in trans, mediated by transient dimerization of their kinase domains. However, motivated by the recently discovered regulation mechanism of activation loop cis-autophosphorylation by a kinase that is autoinhibited in trans, we here review the various mechanisms of autoregulation that have been proposed. We provide a framework for critically evaluating biochemical, kinetic, and structural evidence for protein kinase dimerization and autophosphorylation, and share some thoughts on the implications of these mechanisms within physiological signaling networks.
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Affiliation(s)
- Ronja Reinhardt
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
| | - Thomas A Leonard
- Max Perutz Labs, Vienna Biocenter Campus (VBC)ViennaAustria
- Medical University of Vienna, Center for Medical BiochemistryViennaAustria
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2
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Boonen RA, Wiegant WW, Celosse N, Vroling B, Heijl S, Kote-Jarai Z, Mijuskovic M, Cristea S, Solleveld-Westerink N, van Wezel T, Beerenwinkel N, Eeles R, Devilee P, Vreeswijk MP, Marra G, van Attikum H. Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk. Cancer Res 2022; 82:615-631. [PMID: 34903604 PMCID: PMC9359737 DOI: 10.1158/0008-5472.can-21-1845] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/14/2021] [Accepted: 12/06/2021] [Indexed: 01/07/2023]
Abstract
Heterozygous carriers of germline loss-of-function variants in the tumor suppressor gene checkpoint kinase 2 (CHEK2) are at an increased risk for developing breast and other cancers. While truncating variants in CHEK2 are known to be pathogenic, the interpretation of missense variants of uncertain significance (VUS) is challenging. Consequently, many VUS remain unclassified both functionally and clinically. Here we describe a mouse embryonic stem (mES) cell-based system to quantitatively determine the functional impact of 50 missense VUS in human CHEK2. By assessing the activity of human CHK2 to phosphorylate one of its main targets, Kap1, in Chek2 knockout mES cells, 31 missense VUS in CHEK2 were found to impair protein function to a similar extent as truncating variants, while 9 CHEK2 missense VUS resulted in intermediate functional defects. Mechanistically, most VUS impaired CHK2 kinase function by causing protein instability or by impairing activation through (auto)phosphorylation. Quantitative results showed that the degree of CHK2 kinase dysfunction correlates with an increased risk for breast cancer. Both damaging CHEK2 variants as a group [OR 2.23; 95% confidence interval (CI), 1.62-3.07; P < 0.0001] and intermediate variants (OR 1.63; 95% CI, 1.21-2.20; P = 0.0014) were associated with an increased breast cancer risk, while functional variants did not show this association (OR 1.13; 95% CI, 0.87-1.46; P = 0.378). Finally, a damaging VUS in CHEK2, c.486A>G/p.D162G, was also identified, which cosegregated with familial prostate cancer. Altogether, these functional assays efficiently and reliably identified VUS in CHEK2 that associate with cancer. SIGNIFICANCE Quantitative assessment of the functional consequences of CHEK2 variants of uncertain significance identifies damaging variants associated with increased cancer risk, which may aid in the clinical management of patients and carriers.
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Affiliation(s)
- Rick A.C.M. Boonen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Wouter W. Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Nandi Celosse
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Bas Vroling
- Bio-Prodict, Nijmegen, the Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, Nijmegen, the Netherlands
| | | | | | - Martina Mijuskovic
- The Institute of Cancer Research, London, United Kingdom
- Illumina Cambridge Ltd., Cambridge, United Kingdom
| | - Simona Cristea
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Niko Beerenwinkel
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Rosalind Eeles
- The Institute of Cancer Research, London, United Kingdom
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maaike P.G. Vreeswijk
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Giancarlo Marra
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
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3
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Chen ESW, Weng JH, Chen YH, Wang SC, Liu XX, Huang WC, Matsui T, Kawano Y, Liao JH, Lim LH, Bessho Y, Huang KF, Wu WJ, Tsai MD. Phospho-Priming Confers Functionally Relevant Specificities for Rad53 Kinase Autophosphorylation. Biochemistry 2017; 56:5112-5124. [PMID: 28858528 DOI: 10.1021/acs.biochem.7b00689] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The vast majority of in vitro structural and functional studies of the activation mechanism of protein kinases use the kinase domain alone. Well-demonstrated effects of regulatory domains or allosteric factors are scarce for serine/threonine kinases. Here we use a site-specifically phosphorylated SCD1-FHA1-kinase three-domain construct of the serine/threonine kinase Rad53 to show the effect of phospho-priming, an in vivo regulatory mechanism, on the autophosphorylation intermediate and specificity. Unphosphorylated Rad53 is a flexible monomer in solution but is captured in an asymmetric enzyme:substrate complex in crystal with the two FHA domains separated from each other. Phospho-priming induces formation of a stable dimer via intermolecular pT-FHA binding in solution. Importantly, autophosphorylation of unprimed and phospho-primed Rad53 produced predominantly inactive pS350-Rad53 and active pT354-Rad53, respectively. The latter mechanism was also demonstrated in vivo. Our results show that, while Rad53 can display active conformations under various conditions, simulation of in vivo regulatory conditions confers functionally relevant autophosphorylation.
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Affiliation(s)
- Eric Sheng-Wen Chen
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
| | - Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, Department of Chemistry, National Tsing Hua University , Hsinchu 300, Taiwan
| | - Yu-Hou Chen
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Shun-Chang Wang
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Xiao-Xia Liu
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wei-Cheng Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Tsutomu Matsui
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University , Menlo Park, California 94025, United States
| | - Yoshiaki Kawano
- RIKEN SPring-8 Center , 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Liang-Hin Lim
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
| | - Yoshitaka Bessho
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica , Taipei 115, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei 106, Taiwan
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4
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Raz R, Burlina F, Ismail M, Downward J, Li J, Smerdon SJ, Quibell M, White PD, Offer J. HF-Free Boc Synthesis of Peptide Thioesters for Ligation and Cyclization. Angew Chem Int Ed Engl 2016; 55:13174-13179. [PMID: 27654901 PMCID: PMC5113665 DOI: 10.1002/anie.201607657] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Indexed: 01/03/2023]
Abstract
We have developed a convenient method for the direct synthesis of peptide thioesters, versatile intermediates for peptide ligation and cyclic peptide synthesis. The technology uses a modified Boc SPPS strategy that avoids the use of anhydrous HF. Boc in situ neutralization protocols are used in combination with Merrifield hydroxymethyl resin and TFA/TMSBr cleavage. Avoiding HF extends the scope of Boc SPPS to post-translational modifications that are compatible with the milder cleavage conditions, demonstrated here with the synthesis of the phosphorylated protein CHK2. Peptide thioesters give easy, direct, access to cyclic peptides, illustrated by the synthesis of cyclorasin, a KRAS inhibitor.
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Affiliation(s)
- Richard Raz
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK
| | - Fabienne Burlina
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, Laboratoire des Biomolécules (LBM), Paris, France
- Département de Chimie, ENS, PSL Research University, UPMC, Univ Paris 06, CNRS, LBM, Paris, France
| | - Mohamed Ismail
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK
| | - Julian Downward
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK
| | - Jiejin Li
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK
| | | | - Martin Quibell
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK
| | - Peter D White
- Merck Chemicals, Padge Road, Beeston, Notts, NG9 2JR, UK
| | - John Offer
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK.
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5
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Raz R, Burlina F, Ismail M, Downward J, Li J, Smerdon SJ, Quibell M, White PD, Offer J. HF-Free Boc Synthesis of Peptide Thioesters for Ligation and Cyclization. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Richard Raz
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
| | - Fabienne Burlina
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS; Laboratoire des Biomolécules (LBM); Paris France
- Département de Chimie, ENS; PSL Research University, UPMC, Univ Paris 06, CNRS, LBM; Paris France
| | - Mohamed Ismail
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
| | - Julian Downward
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
| | - Jiejin Li
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
| | | | - Martin Quibell
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
| | | | - John Offer
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
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6
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Weng JH, Hsieh YC, Huang CCF, Wei TYW, Lim LH, Chen YH, Ho MR, Wang I, Huang KF, Chen CJ, Tsai MD. Uncovering the Mechanism of Forkhead-Associated Domain-Mediated TIFA Oligomerization That Plays a Central Role in Immune Responses. Biochemistry 2015; 54:6219-29. [PMID: 26389808 DOI: 10.1021/acs.biochem.5b00500] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Forkhead-associated (FHA) domain is the only signaling domain that recognizes phosphothreonine (pThr) specifically. TRAF-interacting protein with an FHA domain (TIFA) was shown to be involved in immune responses by binding with TRAF2 and TRAF6. We recently reported that TIFA is a dimer in solution and that, upon stimulation by TNF-α, TIFA is phosphorylated at Thr9, which triggers TIFA oligomerization via pThr9-FHA domain binding and activates nuclear factor κB (NF-κB). However, the structural mechanism for the functionally important TIFA oligomerization remains to be established. While FHA domain-pThr binding is known to mediate protein dimerization, its role in oligomerization has not been demonstrated at the structural level. Here we report the crystal structures of TIFA (residues 1-150, with the unstructured C-terminal tail truncated) and its complex with the N-terminal pThr9 peptide (residues 1-15), which show unique features in the FHA structure (intrinsic dimer and extra β-strand) and in its interaction with the pThr peptide (with residues preceding rather than following pThr). These structural features support previous and additional functional analyses. Furthermore, the structure of the complex suggests that the pThr9-FHA domain interaction can occur only between different sets of dimers rather than between the two protomers within a dimer, providing the structural mechanism for TIFA oligomerization. Our results uncover the mechanism of FHA domain-mediated oligomerization in a key step of immune responses and expand the paradigm of FHA domain structure and function.
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Affiliation(s)
- Jui-Hung Weng
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.,Taiwan International Graduate Program, Academia Sinica , Taipei, Taiwan.,Institute of Biochemical Sciences, Department of Chemistry, National Tsing Hua University , Hsinchu, Taiwan
| | - Yin-Cheng Hsieh
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center , Hsinchu, Taiwan
| | - Chia-Chi Flora Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.,Taiwan International Graduate Program, Academia Sinica , Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei, Taiwan
| | - Tong-You Wade Wei
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei, Taiwan
| | - Liang-Hin Lim
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei, Taiwan
| | - Yu-Hou Chen
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan
| | - Iren Wang
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center , Hsinchu, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica , Taipei, Taiwan.,Taiwan International Graduate Program, Academia Sinica , Taipei, Taiwan.,Institute of Biochemical Sciences, National Taiwan University , Taipei, Taiwan
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7
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Chen ESW, Hoch NC, Wang SC, Pellicioli A, Heierhorst J, Tsai MD. Use of quantitative mass spectrometric analysis to elucidate the mechanisms of phospho-priming and auto-activation of the checkpoint kinase Rad53 in vivo. Mol Cell Proteomics 2013; 13:551-65. [PMID: 24302356 PMCID: PMC3916653 DOI: 10.1074/mcp.m113.034058] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The cell cycle checkpoint kinases play central roles in the genome maintenance of eukaryotes. Activation of the yeast checkpoint kinase Rad53 involves Rad9 or Mrc1 adaptor-mediated phospho-priming by Mec1 kinase, followed by auto-activating phosphorylation within its activation loop. However, the mechanisms by which these adaptors regulate priming phosphorylation of specific sites and how this then leads to Rad53 activation remain poorly understood. Here we used quantitative mass spectrometry to delineate the stepwise phosphorylation events in the activation of endogenous Rad53 in response to S phase alkylation DNA damage, and we show that the two Rad9 and Mrc1 adaptors, the four N-terminal Mec1-target TQ sites of Rad53 (Rad53-SCD1), and Rad53-FHA2 coordinate intimately for optimal priming phosphorylation to support substantial Rad53 auto-activation. Rad9 or Mrc1 alone can mediate surprisingly similar Mec1 target site phosphorylation patterns of Rad53, including previously undetected tri- and tetraphosphorylation of Rad53-SCD1. Reducing the number of TQ motifs turns the SCD1 into a proportionally poorer Mec1 target, which then requires the presence of both Mrc1 and Rad9 for sufficient priming and auto-activation. The phosphothreonine-interacting Rad53-FHA domains, particularly FHA2, regulate phospho-priming by interacting with the checkpoint mediators but do not seem to play a major role in the phospho-SCD1-dependent auto-activation step. Finally, mutation of all four SCD1 TQ motifs greatly reduces Rad53 activation but does not eliminate it, and residual Rad53 activity in this mutant is dependent on Rad9 but not Mrc1. Altogether, our results provide a paradigm for how phosphorylation site clusters and checkpoint mediators can be involved in the regulation of signaling relay in protein kinase cascades in vivo and elucidate an SCD1-independent Rad53 auto-activation mechanism through the Rad9 pathway. The work also demonstrates the power of mass spectrometry for in-depth analyses of molecular mechanisms in cellular signaling in vivo.
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Affiliation(s)
- Eric S-W Chen
- Institute of Biological Chemistry, Taipei 115, Taiwan
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8
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1 0 6. Cancer Biomark 2012. [DOI: 10.1201/b14318-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Intermolecular binding between TIFA-FHA and TIFA-pT mediates tumor necrosis factor alpha stimulation and NF-κB activation. Mol Cell Biol 2012; 32:2664-73. [PMID: 22566686 DOI: 10.1128/mcb.00438-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The forkhead-associated (FHA) domain recognizes phosphothreonine (pT) with high specificity and functional diversity. TIFA (TRAF-interacting protein with an FHA domain) is the smallest FHA-containing human protein. Its overexpression was previously suggested to provoke NF-κB activation, yet its exact roles in this signaling pathway and the underlying molecular mechanism remain unclear. Here we identify a novel threonine phosphorylation site on TIFA and show that this phosphorylated threonine (pT) binds with the FHA domain of TIFA, leading to TIFA oligomerization and TIFA-mediated NF-κB activation. Detailed analysis indicated that unphosphorylated TIFA exists as an intrinsic dimer and that the FHA-pT9 binding occurs between different dimers of TIFA. In addition, silencing of endogenous TIFA resulted in attenuation of tumor necrosis factor alpha (TNF-α)-mediated downstream signaling. We therefore propose that the TIFA FHA-pT9 binding provides a previously unidentified link between TNF-α stimulation and NF-κB activation. The intermolecular FHA-pT9 binding between dimers also represents a new mechanism for the FHA domain.
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10
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Jungmichel S, Clapperton JA, Lloyd J, Hari FJ, Spycher C, Pavic L, Li J, Haire LF, Bonalli M, Larsen DH, Lukas C, Lukas J, MacMillan D, Nielsen ML, Stucki M, Smerdon SJ. The molecular basis of ATM-dependent dimerization of the Mdc1 DNA damage checkpoint mediator. Nucleic Acids Res 2012; 40:3913-28. [PMID: 22234878 PMCID: PMC3351161 DOI: 10.1093/nar/gkr1300] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mdc1 is a large modular phosphoprotein scaffold that maintains signaling and repair complexes at double-stranded DNA break sites. Mdc1 is anchored to damaged chromatin through interaction of its C-terminal BRCT-repeat domain with the tail of γH2AX following DNA damage, but the role of the N-terminal forkhead-associated (FHA) domain remains unclear. We show that a major binding target of the Mdc1 FHA domain is a previously unidentified DNA damage and ATM-dependent phosphorylation site near the N-terminus of Mdc1 itself. Binding to this motif stabilizes a weak self-association of the FHA domain to form a tight dimer. X-ray structures of free and complexed Mdc1 FHA domain reveal a 'head-to-tail' dimerization mechanism that is closely related to that seen in pre-activated forms of the Chk2 DNA damage kinase, and which both positively and negatively influences Mdc1 FHA domain-mediated interactions in human cells prior to and following DNA damage.
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Affiliation(s)
- Stephanie Jungmichel
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich - Irchel, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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11
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Burlina F, Morris C, Behrendt R, White P, Offer J. Simplifying native chemical ligation with an N-acylsulfonamide linker. Chem Commun (Camb) 2012; 48:2579-81. [DOI: 10.1039/c2cc15911b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Macmillan D, Adams A, Premdjee B. Shifting Native Chemical Ligation into Reverse through N→S Acyl Transfer. Isr J Chem 2011; 51:885-899. [PMID: 22347724 PMCID: PMC3277902 DOI: 10.1002/ijch.201100084] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 08/27/2011] [Indexed: 11/06/2022]
Abstract
Peptide thioester synthesis by N→S acyl transfer is being intensively explored by many research groups the world over. Reasons for this likely include the often straightforward method of precursor assembly using Fmoc-based chemistry and the fundamentally interesting acyl migration process. In this review we introduce recent advances in this exciting area and discuss, in more detail, our own efforts towards the synthesis of peptide thioesters through N→S acyl transfer in native peptide sequences. We have found that several peptide thioesters can be readily prepared and, what's more, there appears to be ample opportunity for further development and discovery.
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Affiliation(s)
- Derek Macmillan
- Christopher Ingold Laboratories, Department of Chemistry, University College London20 Gordon Street, London WC1H 0AJ, UK phone: +44 (0)20 7679 4684 e-mail:
| | - Anna Adams
- Christopher Ingold Laboratories, Department of Chemistry, University College London20 Gordon Street, London WC1H 0AJ, UK phone: +44 (0)20 7679 4684 e-mail:
| | - Bhavesh Premdjee
- Christopher Ingold Laboratories, Department of Chemistry, University College London20 Gordon Street, London WC1H 0AJ, UK phone: +44 (0)20 7679 4684 e-mail:
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13
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Spivey VL, Molle V, Whalan RH, Rodgers A, Leiba J, Stach L, Walker KB, Smerdon SJ, Buxton RS. Forkhead-associated (FHA) domain containing ABC transporter Rv1747 is positively regulated by Ser/Thr phosphorylation in Mycobacterium tuberculosis. J Biol Chem 2011; 286:26198-209. [PMID: 21622570 PMCID: PMC3138270 DOI: 10.1074/jbc.m111.246132] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/24/2011] [Indexed: 12/22/2022] Open
Abstract
One major signaling method employed by Mycobacterium tuberculosis, the causative agent of tuberculosis, is through reversible phosphorylation of proteins mediated by protein kinases and phosphatases. This study concerns one of these enzymes, the serine/threonine protein kinase PknF, that is encoded in an operon with Rv1747, an ABC transporter that is necessary for growth of M. tuberculosis in vivo and contains two forkhead-associated (FHA) domains. FHA domains are phosphopeptide recognition motifs that specifically recognize phosphothreonine-containing epitopes. Experiments to determine how PknF regulates the function of Rv1747 demonstrated that phosphorylation occurs on two specific threonine residues, Thr-150 and Thr-208. To determine the in vivo consequences of phosphorylation, infection experiments were performed in bone marrow-derived macrophages and in mice using threonine-to-alanine mutants of Rv1747 that prevent specific phosphorylation and revealed that phosphorylation positively modulates Rv1747 function in vivo. The role of the FHA domains in this regulation was further demonstrated by isothermal titration calorimetry, using peptides containing both phosphothreonine residues. FHA-1 domain mutation resulted in attenuation in macrophages highlighting the critical role of this domain in Rv1747 function. A mutant deleted for pknF did not, however, have a growth phenotype in an infection, suggesting that other kinases can fulfill its role when it is absent. This study provides the first information on the molecular mechanism(s) regulating Rv1747 through PknF-dependent phosphorylation but also indicates that phosphorylation activates Rv1747, which may have important consequences in regulating growth of M. tuberculosis.
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Affiliation(s)
- Vicky L. Spivey
- From the Division of Mycobacterial Research, Medical Research Council National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Virginie Molle
- the Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Universités de Montpellier II et I, CNRS, UMR 5235, Case 107, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Rachael H. Whalan
- From the Division of Mycobacterial Research, Medical Research Council National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Angela Rodgers
- the Immunology and Cellular Immunity Section, Bacteriology Division, National Institute of Biological Standards and Control (A Centre of the Health Protection Agency), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom, and
| | - Jade Leiba
- the Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Universités de Montpellier II et I, CNRS, UMR 5235, Case 107, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - Lasse Stach
- the Division of Molecular Structure, Medical Research Council National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - K. Barry Walker
- the Immunology and Cellular Immunity Section, Bacteriology Division, National Institute of Biological Standards and Control (A Centre of the Health Protection Agency), Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, United Kingdom, and
| | - Stephen J. Smerdon
- the Division of Molecular Structure, Medical Research Council National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
| | - Roger S. Buxton
- From the Division of Mycobacterial Research, Medical Research Council National Institute for Medical Research, Mill Hill, London NW7 1AA, United Kingdom
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CHEK2 genomic and proteomic analyses reveal genetic inactivation or endogenous activation across the 60 cell lines of the US National Cancer Institute. Oncogene 2011; 31:403-18. [PMID: 21765476 DOI: 10.1038/onc.2011.283] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
CHEK2 encodes a serine/threonine kinase (Chk2) activated by ATM in response to DNA double-strand breaks. On the one hand, CHEK2 has been described as a tumor suppressor with proapoptotic, cell-cycle checkpoint and mitotic functions. On the other hand, Chk2 is also commonly activated (phosphorylated at T68) in cancers and precancerous lesions. Here, we report an extensive characterization of CHEK2 across the panel of 60 established cancer cell lines from the NCI Anticancer Screen (the NCI-60) using genomic and proteomic analyses, including exon-specific mRNA expression, DNA copy-number variation (CNV) by aCGH, exome sequencing, as well as western blot analyses for total and activated (pT68-Chk2) Chk2. We show that the high heterogeneity of Chk2 levels in cancer cells is primarily due to its inactivation (owing to low gene expression, alternative splicing, point mutations, copy-number alterations and premature truncation) or reduction of protein levels. Moreover, we observe that a significant percentage of cancer cells (12% of the NCI-60 and HeLa cells) show high endogenous Chk2 activation, which is always associated with p53 inactivation, and which is accompanied by downregulation of the Fanconi anemia and homologous recombination pathways. We also report the presence of activated Chk2 (pT68-Chk2) along with histone γ-H2AX in centrosomes.
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15
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Abstract
There is mounting evidence that replication defects are the major source of spontaneous genomic instability in cells, and that S-phase checkpoints are the principal defense against such instability. The S-phase checkpoint mediator protein Mrc1/Claspin mediates the checkpoint response to replication stress by facilitating phosphorylation of effector kinase by a sensor kinase. In this review, the multiple functions and the regulation of the S-phase checkpoint mediator are discussed.
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16
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MDC1: The art of keeping things in focus. Chromosoma 2010; 119:337-49. [PMID: 20224865 DOI: 10.1007/s00412-010-0266-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 02/05/2010] [Accepted: 02/14/2010] [Indexed: 10/19/2022]
Abstract
The chromatin structure is important for recognition and repair of DNA damage. Many DNA damage response proteins accumulate in large chromatin domains flanking sites of DNA double-strand breaks. The assembly of these structures-usually termed DNA damage foci-is primarily regulated by MDC1, a large nuclear mediator/adaptor protein that is composed of several distinct structural and functional domains. Here, we are summarizing the latest discoveries about the mechanisms by which MDC1 mediates DNA damage foci formation, and we are reviewing the considerable efforts taken to understand the functional implication of these structures.
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17
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Rich RL, Myszka DG. Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'. J Mol Recognit 2010; 23:1-64. [PMID: 20017116 DOI: 10.1002/jmr.1004] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Optical biosensor technology continues to be the method of choice for label-free, real-time interaction analysis. But when it comes to improving the quality of the biosensor literature, education should be fundamental. Of the 1413 articles published in 2008, less than 30% would pass the requirements for high-school chemistry. To teach by example, we spotlight 10 papers that illustrate how to implement the technology properly. Then we grade every paper published in 2008 on a scale from A to F and outline what features make a biosensor article fabulous, middling or abysmal. To help improve the quality of published data, we focus on a few experimental, analysis and presentation mistakes that are alarmingly common. With the literature as a guide, we want to ensure that no user is left behind.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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18
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van Vugt MATM, Gardino AK, Linding R, Ostheimer GJ, Reinhardt HC, Ong SE, Tan CS, Miao H, Keezer SM, Li J, Pawson T, Lewis TA, Carr SA, Smerdon SJ, Brummelkamp TR, Yaffe MB. A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint. PLoS Biol 2010; 8:e1000287. [PMID: 20126263 PMCID: PMC2811157 DOI: 10.1371/journal.pbio.1000287] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 12/11/2009] [Indexed: 12/18/2022] Open
Abstract
DNA damage checkpoints arrest cell cycle progression to facilitate DNA repair. The ability to survive genotoxic insults depends not only on the initiation of cell cycle checkpoints but also on checkpoint maintenance. While activation of DNA damage checkpoints has been studied extensively, molecular mechanisms involved in sustaining and ultimately inactivating cell cycle checkpoints are largely unknown. Here, we explored feedback mechanisms that control the maintenance and termination of checkpoint function by computationally identifying an evolutionary conserved mitotic phosphorylation network within the DNA damage response. We demonstrate that the non-enzymatic checkpoint adaptor protein 53BP1 is an in vivo target of the cell cycle kinases Cyclin-dependent kinase-1 and Polo-like kinase-1 (Plk1). We show that Plk1 binds 53BP1 during mitosis and that this interaction is required for proper inactivation of the DNA damage checkpoint. 53BP1 mutants that are unable to bind Plk1 fail to restart the cell cycle after ionizing radiation-mediated cell cycle arrest. Importantly, we show that Plk1 also phosphorylates the 53BP1-binding checkpoint kinase Chk2 to inactivate its FHA domain and inhibit its kinase activity in mammalian cells. Thus, a mitotic kinase-mediated negative feedback loop regulates the ATM-Chk2 branch of the DNA damage signaling network by phosphorylating conserved sites in 53BP1 and Chk2 to inactivate checkpoint signaling and control checkpoint duration.
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Affiliation(s)
- Marcel A. T. M. van Vugt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Alexandra K. Gardino
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Rune Linding
- Cellular and Molecular Logic Team Integrative Network Biology initiative (INBi) Section of Cell and Molecular Biology, The Institute of Cancer Research, London, United Kingdom
| | - Gerard J. Ostheimer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Departments of Biological Engineering and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - H. Christian Reinhardt
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Shao-En Ong
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Chris S. Tan
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Hua Miao
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Susan M. Keezer
- Cell Signaling Technologies, Danvers, Massachusetts, United States of America
| | - Jeijin Li
- Division of Molecular Structure, Medical Research Council (MRC) National Institute for Medical Research, London, United Kingdom
| | - Tony Pawson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Timothy A. Lewis
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Steven A. Carr
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
| | - Stephen J. Smerdon
- Division of Molecular Structure, Medical Research Council (MRC) National Institute for Medical Research, London, United Kingdom
| | - Thijn R. Brummelkamp
- Whitehead Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Michael B. Yaffe
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Departments of Biological Engineering and Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
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19
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Masania J, Li J, Smerdon SJ, Macmillan D. Access to phosphoproteins and glycoproteins through semi-synthesis, Native Chemical Ligation and N→S acyl transfer. Org Biomol Chem 2010; 8:5113-9. [DOI: 10.1039/c0ob00363h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Liu L, Rao JN, Zou T, Xiao L, Wang PY, Turner DJ, Gorospe M, Wang JY. Polyamines regulate c-Myc translation through Chk2-dependent HuR phosphorylation. Mol Biol Cell 2009; 20:4885-98. [PMID: 19812253 DOI: 10.1091/mbc.e09-07-0550] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
All mammalian cells depend on polyamines for normal growth and proliferation, but the exact roles of polyamines at the molecular level remain largely unknown. The RNA-binding protein HuR modulates the stability and translation of many target mRNAs. Here, we show that in rat intestinal epithelial cells (IECs), polyamines enhanced HuR association with the 3'-untranslated region of the c-Myc mRNA by increasing HuR phosphorylation by Chk2, in turn promoting c-Myc translation. Depletion of cellular polyamines inhibited Chk2 and reduced the affinity of HuR for c-Myc mRNA; these effects were completely reversed by addition of the polyamine putrescine or by Chk2 overexpression. In cells with high content of cellular polyamines, HuR silencing or Chk2 silencing reduced c-Myc translation and c-Myc expression levels. Our findings demonstrate that polyamines regulate c-Myc translation in IECs through HuR phosphorylation by Chk2 and provide new insight into the molecular functions of cellular polyamines.
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Affiliation(s)
- Lan Liu
- Cell Biology Group, Department of Surgery, and Department of Pathology, University of Maryland School of Medicine and Baltimore Veterans Affairs Medical Center, Baltimore, MD 21201, USA
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21
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Structure and Activation Mechanism of the CHK2 DNA Damage Checkpoint Kinase. Mol Cell 2009; 35:818-29. [DOI: 10.1016/j.molcel.2009.09.007] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 06/26/2009] [Accepted: 07/25/2009] [Indexed: 11/19/2022]
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22
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Xu YJ, Kelly TJ. Autoinhibition and autoactivation of the DNA replication checkpoint kinase Cds1. J Biol Chem 2009; 284:16016-27. [PMID: 19357077 PMCID: PMC2708895 DOI: 10.1074/jbc.m900785200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 03/30/2009] [Indexed: 11/06/2022] Open
Abstract
Cds1 is the ortholog of Chk2 and the major effector of the DNA replication checkpoint in Schizosaccharomyces pombe. Previous studies have shown that Cds1 is activated by a two-stage mechanism. In the priming stage, the sensor kinase Rad3 and the mediator Mrc1 function to phosphorylate a threonine residue, Thr(11), in the SQ/TQ domain of Cds1. In the autoactivation stage, primed Cds1 molecules dimerize via intermolecular interactions between the phosphorylated Thr(11) in one Cds1 and the forkhead-associated domain of the other. Dimerization activates Cds1, probably by promoting autophosphorylation. To define the mechanisms for the autoactivation of primed Cds1 and the regulation of this process, we carried out genetic and biochemical studies to identify phosphorylatable residues required for checkpoint activation. Our data indicate that dimerization of Cds1 promotes trans-autophosphorylation of a number of residues in the catalytic domain, but phosphorylation of a highly conserved threonine residue (Thr(328)) in the activation loop is the only covalent modification required for kinase activation in vitro and in vivo. Autophosphorylation of Thr(328) and kinase activation in unprimed, monomeric Cds1 are strongly inhibited by the C-terminal 27-amino acid tail of the enzyme. This autoinhibitory effect may play an important role in preventing spontaneous activation of the replication checkpoint during normal cell cycles. The two-stage activation pathway and the autoinhibition mechanism, which are probably shared by other members of the Chk2 family, provide sensitivity, specificity, and noise immunity, properties required for the replication checkpoint.
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Affiliation(s)
- Yong-jie Xu
- From the Program in Molecular Biology, Sloan-Kettering Institute, New York, New York 10021 and the
- Department of Biochemistry and Molecular Biology, Wright State University School of Medicine, Dayton, Ohio 45435
| | - Thomas J. Kelly
- From the Program in Molecular Biology, Sloan-Kettering Institute, New York, New York 10021 and the
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23
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Mohammad DH, Yaffe MB. 14-3-3 proteins, FHA domains and BRCT domains in the DNA damage response. DNA Repair (Amst) 2009; 8:1009-17. [PMID: 19481982 DOI: 10.1016/j.dnarep.2009.04.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The DNA damage response depends on the concerted activity of protein serine/threonine kinases and modular phosphoserine/threonine-binding domains to relay the damage signal and recruit repair proteins. The PIKK family of protein kinases, which includes ATM/ATR/DNA-PK, preferentially phosphorylate Ser-Gln sites, while their basophilic downstream effecter kinases, Chk1/Chk2/MK2 preferentially phosphorylate hydrophobic-X-Arg-X-X-Ser/Thr-hydrophobic sites. A subset of tandem BRCT domains act as phosphopeptide binding modules that bind to ATM/ATR/DNA-PK substrates after DNA damage. Conversely, 14-3-3 proteins interact with substrates of Chk1/Chk2/MK2. FHA domains have been shown to interact with substrates of ATM/ATR/DNA-PK and CK2. In this review we consider how substrate phosphorylation together with BRCT domains, FHA domains and 14-3-3 proteins function to regulate ionizing radiation-induced nuclear foci and help to establish the G(2)/M checkpoint. We discuss the role of MDC1 a molecular scaffold that recruits early proteins to foci, such as NBS1 and RNF8, through distinct phosphodependent interactions. In addition, we consider the role of 14-3-3 proteins and the Chk2 FHA domain in initiating and maintaining cell cycle arrest.
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Affiliation(s)
- Duaa H Mohammad
- David H. Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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24
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Stern DF. BRCTing up is hard to do. Mol Cell 2009; 33:137-8. [PMID: 19187753 DOI: 10.1016/j.molcel.2009.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this issue of Molecular Cell, Usui et al. (2009) show that Mec1-phosphorylated Rad9 SCD interacts with the BRCT domain, promoting oligomerization. This sustains the DNA damage checkpoint and is suppressed by Rad53 phosphorylation in a negative feedback circuit.
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Affiliation(s)
- David F Stern
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520-8023, USA.
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