Imperial College London

Dr Luke A. Yates

Faculty of MedicineDepartment of Infectious Disease

Research Associate
 
 
 
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luke.yates

 
 
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245Sir Alexander Fleming BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

10 results found

Yates LA, 2021, Regulation of DNA break repair by RNA, PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, Vol: 163, Pages: 23-33, ISSN: 0079-6107

Journal article

Tannous EA, Yates LA, Zhang X, Burgers PMet al., 2021, Mechanism of auto-inhibition and activation of Mec1ATR checkpoint kinase, Nature Structural and Molecular Biology, Vol: 28, Pages: 50-61, ISSN: 1545-9985

In response to DNA damage or replication fork stalling, the basal activity of Mec1ATR is stimulated in a cell-cycle-dependent manner, leading to cell-cycle arrest and the promotion of DNA repair. Mec1ATR dysfunction leads to cell death in yeast and causes chromosome instability and embryonic lethality in mammals. Thus, ATR is a major target for cancer therapies in homologous recombination-deficient cancers. Here we identify a single mutation in Mec1, conserved in ATR, that results in constitutive activity. Using cryo-electron microscopy, we determine the structures of this constitutively active form (Mec1(F2244L)-Ddc2) at 2.8 Å and the wild type at 3.8 Å, both in complex with Mg2+-AMP-PNP. These structures yield a near-complete atomic model for Mec1-Ddc2 and uncover the molecular basis for low basal activity and the conformational changes required for activation. Combined with biochemical and genetic data, we discover key regulatory regions and propose a Mec1 activation mechanism.

Journal article

Williams R, Yates L, Zhang X, 2020, Structures and regulations of ATM and ATR, master kinases in genome integrity, Current Opinion in Structural Biology, Vol: 61, Pages: 98-105, ISSN: 0959-440X

Homologous recombination (HR) is a faithful repair mechanism for double stranded DNA breaks. Two highly homologous master kinases, the tumour suppressors ATM and ATR (Tel1 and Mec1 in yeast), coordinate cell cycle progression with repair during HR. Despite their importance, our molecular understanding of these apical coordinators has been limited, in part due to their large sizes. With the recent development in cryo-electron microscopy, significant advances have been made in structural characterisation of these proteins in the last two years. These structures, combined with new biochemical studies, now provide a more detailed understanding of how a low basal activity is maintained and how activation may occur. In this review, we summarize recent advances in the structural and molecular understanding of these key components in HR, compare the common and distinct features of these kinases and suggest aspects of structural components that are likely to be involved in regulating its activity.

Journal article

Yates L, Williams R, Hailemariam S, Ayala R, Zhang Xet al., 2020, Cryo-EM structure of nucleotide-bound Tel1ATM unravels the molecular basis of inhibition and structural rationale for disease-associated mutations, Structure, Vol: 28, Pages: 96-104.e3, ISSN: 0969-2126

Yeast Tel1 and its highly conserved human orthologue ATM are large protein kinases centralto the maintenance of genome integrity. Mutations in ATM are found in ataxia-telangiectasia(A-T) patients and ATM is one of the most frequently mutated genes in many cancers. Usingcryo electron microscopy, we present the structure of Tel1 in a nucleotide-bound state. Ourstructure reveals molecular details of key residues surrounding the nucleotide binding site andprovides a structural and molecular basis for its intrinsically low basal activity. We show thatthe catalytic residues are in a productive conformation for catalysis, but the PIKK-regulatorydomain-Insert (PRD-I) restricts peptide-substrate access and the N-lobe is in an openconformation, thus explaining the requirement for Tel1 activation. Structural comparisons withother PIKKs suggest a conserved and common allosteric activation mechanism. Our work alsoprovides a structural rationale for many mutations found in A-T and cancer.

Journal article

Sun Y, McCorvie TJ, Yates LA, Zhang Xet al., 2019, Structural basis of homologous recombination, CELLULAR AND MOLECULAR LIFE SCIENCES, Vol: 77, Pages: 3-18, ISSN: 1420-682X

Journal article

Yates LA, Williams RM, Hailemariam S, Ayala R, Burgers P, Zhang Xet al., 2019, Structure of nucleotide-bound Tel1ATM reveals the molecular basis of inhibition and structural rationale for disease mutations

<jats:sec><jats:title>SUMMARY</jats:title><jats:p>Yeast Tel1 and its highly conserved human orthologue ATM are large protein kinases central to the maintenance of genome integrity. Mutations in ATM are found in ataxia-telangiectasia (A-T) patients and ATM is one of the most frequently mutated genes in many cancers. Using cryo electron microscopy, we present the structure of Tel1 in a nucleotide-bound state. Our structure reveals molecular details of key residues surrounding the nucleotide binding site and provides a structural and molecular basis for its intrinsically low basal activity. We show that the catalytic residues are in a productive conformation for catalysis, but the PIKK-regulatory domain-Insert (PRD-I) restricts peptide-substrate access and the N-lobe is in an open conformation, thus explaining the requirement for Tel1 activation. Structural comparisons with other PIKKs suggest a conserved and common allosteric activation mechanism. Our work also provides a structural rationale for many mutations found in A-T and cancer.</jats:p></jats:sec>

Journal article

Abdul-Salam V, Russomanno G, Chien-Nien C, Mahomed A, Yates L, Wilkins M, Zhao L, Gierula M, Dubois O, Schaeper U, Endruschat J, Wojciak-Stothard Bet al., 2019, CLIC4/Arf6 pathway – a new lead in BMPRII inhibition in pulmonary hypertension, Circulation Research, Vol: 124, Pages: 52-65, ISSN: 0009-7330

Rationale:Increased expression of CLIC4 (chloride intracellular channel 4) is a feature of endothelial dysfunction in pulmonary arterial hypertension, but its role in disease pathology is not fully understood.Objective:To identify CLIC4 effectors and evaluate strategies targeting CLIC4 signaling in pulmonary hypertension.Methods and Results:Proteomic analysis of CLIC4-interacting proteins in human pulmonary artery endothelial cells identified regulators of endosomal trafficking, including Arf6 (ADP ribosylation factor 6) GTPase activating proteins and clathrin, while CLIC4 overexpression affected protein regulators of vesicular trafficking, lysosomal function, and inflammation. CLIC4 reduced BMPRII (bone morphogenetic protein receptor II) expression and signaling as a result of Arf6-mediated reduction in gyrating clathrin and increased lysosomal targeting of the receptor. BMPRII expression was restored by Arf6 siRNA, Arf inhibitor Sec7 inhibitor H3 (SecinH3), and inhibitors of clathrin-mediated endocytosis but was unaffected by chloride channel inhibitor, indanyloxyacetic acid 94 or Arf1 siRNA. The effects of CLIC4 on NF-κB (nuclear factor-kappa B), HIF (hypoxia-inducible factor), and angiogenic response were prevented by Arf6 siRNA and SecinH3. Sugen/hypoxia mice and monocrotaline rats showed elevated expression of CLIC4, activation of Arf6 and NF-κB, and reduced expression of BMPRII in the lung. These changes were established early during disease development. Lung endothelium–targeted delivery of CLIC4 siRNA or treatment with SecinH3 attenuated the disease, reduced CLIC4/Arf activation, and restored BMPRII expression in the lung. Endothelial colony–forming cells from idiopathic pulmonary hypertensive patients showed upregulation of CLIC4 expression and Arf6 activity, suggesting potential importance of this pathway in the human condition.Conclusions:Arf6 is a novel effector of CLIC4 and a new therapeutic target in pulmonary hypertension.

Journal article

Yates LA, Aramayo RJ, Pokhrel N, Caldwell CC, Kaplan JA, Perera RL, Spies M, Anthony E, Zhang Xet al., 2018, A structural and dynamic model for the assembly of Replication Protein A on single-stranded DNA, Nature Communications, Vol: 9, ISSN: 2041-1723

Replication Protein A (RPA), the major eukaryotic single stranded DNA-binding protein, binds to exposed ssDNA to protect it from nucleases, participates in a myriad of nucleic acid transactions and coordinates the recruitment of other important players. RPA is a heterotrimer and coats long stretches of single-stranded DNA (ssDNA). The precise molecular architecture of the RPA subunits and its DNA binding domains (DBDs) during assembly is poorly understood. Using cryo electron microscopy we obtained a 3D reconstruction of the RPA trimerisation core bound with ssDNA (∼55 kDa) at ∼4.7 Å resolution and a dimeric RPA assembly on ssDNA. FRET-based solution studies reveal dynamic rearrangements of DBDs during coordinated RPA binding and this activity is regulated by phosphorylation at S178 in RPA70. We present a structural model on how dynamic DBDs promote the cooperative assembly of multiple RPAs on long ssDNA.

Journal article

Ni T, Kalli AC, Naughton FB, Yates LA, Naneh O, Kozorog M, Anderluh G, Sansom MSP, Gilbert RJCet al., 2017, Structure and lipid-binding properties of the kindlin-3 pleckstrin homology domain, BIOCHEMICAL JOURNAL, Vol: 474, Pages: 539-556, ISSN: 0264-6021

Journal article

Feng T, Yamamoto A, Wilkins SE, Sokolova E, Yates LA, Münzel M, Singh P, Hopkinson RJ, Fischer R, Cockman ME, Shelley J, Trudgian DC, Schödel J, McCullagh JSO, Ge W, Kessler BM, Gilbert RJ, Frolova LY, Alkalaeva E, Ratcliffe PJ, Schofield CJ, Coleman MLet al., 2014, Optimal translational termination requires C4 lysyl hydroxylation of eRF1., Mol Cell, Vol: 53, Pages: 645-654

Efficient stop codon recognition and peptidyl-tRNA hydrolysis are essential in order to terminate translational elongation and maintain protein sequence fidelity. Eukaryotic translational termination is mediated by a release factor complex that includes eukaryotic release factor 1 (eRF1) and eRF3. The N terminus of eRF1 contains highly conserved sequence motifs that couple stop codon recognition at the ribosomal A site to peptidyl-tRNA hydrolysis. We reveal that Jumonji domain-containing 4 (Jmjd4), a 2-oxoglutarate- and Fe(II)-dependent oxygenase, catalyzes carbon 4 (C4) lysyl hydroxylation of eRF1. This posttranslational modification takes place at an invariant lysine within the eRF1 NIKS motif and is required for optimal translational termination efficiency. These findings further highlight the role of 2-oxoglutarate/Fe(II) oxygenases in fundamental cellular processes and provide additional evidence that ensuring fidelity of protein translation is a major role of hydroxylation.

Journal article

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