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Caspers NL, Han S, Rajamohan F, Hoth LR, Geoghegan KF, Subashi TA, Vazquez ML, Kaila N, Cronin CN, Johnson E, Kurumbail RG. Development of a high-throughput crystal structure-determination platform for JAK1 using a novel metal-chelator soaking system. Acta Crystallogr F Struct Biol Commun 2016; 72:840-845. [PMID: 27827355 PMCID: PMC5101585 DOI: 10.1107/s2053230x16016356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/13/2016] [Indexed: 11/11/2022] Open
Abstract
Crystals of phosphorylated JAK1 kinase domain were initially generated in complex with nucleotide (ADP) and magnesium. The tightly bound Mg2+-ADP at the ATP-binding site proved recalcitrant to ligand displacement. Addition of a molar excess of EDTA helped to dislodge the divalent metal ion, promoting the release of ADP and allowing facile exchange with ATP-competitive small-molecule ligands. Many kinases require the presence of a stabilizing ligand in the ATP site for crystallization. This procedure could be useful for developing co-crystallization systems with an exchangeable ligand to enable structure-based drug design of other protein kinases.
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Affiliation(s)
- Nicole L. Caspers
- Structural Biology, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Seungil Han
- Structural Biology, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Francis Rajamohan
- Structural Biology, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Lise R. Hoth
- Structural Biology, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | | | - Timothy A. Subashi
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
| | - Michael L. Vazquez
- Inflammation Medicinal Chemistry, Pfizer Inc., 610 Main Street, Cambridge, MA 02139, USA
| | - Neelu Kaila
- Inflammation Medicinal Chemistry, Pfizer Inc., 610 Main Street, Cambridge, MA 02139, USA
| | - Ciarán N. Cronin
- Oncology Structural Biology, Pfizer Inc., 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Eric Johnson
- Oncology Structural Biology, Pfizer Inc., 10770 Science Center Drive, San Diego, CA 92121, USA
| | - Ravi G. Kurumbail
- Structural Biology, Pfizer Inc., Eastern Point Road, Groton, CT 06340, USA
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A robust methodology to subclassify pseudokinases based on their nucleotide-binding properties. Biochem J 2014; 457:323-34. [PMID: 24107129 DOI: 10.1042/bj20131174] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein kinase-like domains that lack conserved residues known to catalyse phosphoryl transfer, termed pseudokinases, have emerged as important signalling domains across all kingdoms of life. Although predicted to function principally as catalysis-independent protein-interaction modules, several pseudokinase domains have been attributed unexpected catalytic functions, often amid controversy. We established a thermal-shift assay as a benchmark technique to define the nucleotide-binding properties of kinase-like domains. Unlike in vitro kinase assays, this assay is insensitive to the presence of minor quantities of contaminating kinases that may otherwise lead to incorrect attribution of catalytic functions to pseudokinases. We demonstrated the utility of this method by classifying 31 diverse pseudokinase domains into four groups: devoid of detectable nucleotide or cation binding; cation-independent nucleotide binding; cation binding; and nucleotide binding enhanced by cations. Whereas nine pseudokinases bound ATP in a divalent cation-dependent manner, over half of those examined did not detectably bind nucleotides, illustrating that pseudokinase domains predominantly function as non-catalytic protein-interaction modules within signalling networks and that only a small subset is potentially catalytically active. We propose that henceforth the thermal-shift assay be adopted as the standard technique for establishing the nucleotide-binding and catalytic potential of kinase-like domains.
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Linossi EM, Chandrashekaran IR, Kolesnik TB, Murphy JM, Webb AI, Willson TA, Kedzierski L, Bullock AN, Babon JJ, Norton RS, Nicola NA, Nicholson SE. Suppressor of Cytokine Signaling (SOCS) 5 utilises distinct domains for regulation of JAK1 and interaction with the adaptor protein Shc-1. PLoS One 2013; 8:e70536. [PMID: 23990909 PMCID: PMC3749136 DOI: 10.1371/journal.pone.0070536] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 06/20/2013] [Indexed: 12/02/2022] Open
Abstract
Suppressor of Cytokine Signaling (SOCS)5 is thought to act as a tumour suppressor through negative regulation of JAK/STAT and epidermal growth factor (EGF) signaling. However, the mechanism/s by which SOCS5 acts on these two distinct pathways is unclear. We show for the first time that SOCS5 can interact directly with JAK via a unique, conserved region in its N-terminus, which we have termed the JAK interaction region (JIR). Co-expression of SOCS5 was able to specifically reduce JAK1 and JAK2 (but not JAK3 or TYK2) autophosphorylation and this function required both the conserved JIR and additional sequences within the long SOCS5 N-terminal region. We further demonstrate that SOCS5 can directly inhibit JAK1 kinase activity, although its mechanism of action appears distinct from that of SOCS1 and SOCS3. In addition, we identify phosphoTyr317 in Shc-1 as a high-affinity substrate for the SOCS5-SH2 domain and suggest that SOCS5 may negatively regulate EGF and growth factor-driven Shc-1 signaling by binding to this site. These findings suggest that different domains in SOCS5 contribute to two distinct mechanisms for regulation of cytokine and growth factor signaling.
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Affiliation(s)
- Edmond M. Linossi
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Indu R. Chandrashekaran
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Tatiana B. Kolesnik
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - James M. Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew I. Webb
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Tracy A. Willson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Lukasz Kedzierski
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Alex N. Bullock
- Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom
| | - Jeffrey J. Babon
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Raymond S. Norton
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Nicos A. Nicola
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
| | - Sandra E. Nicholson
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- The University of Melbourne, Parkville, Victoria, Australia
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