5d7v

From Proteopedia

(Difference between revisions)

Revision as of 00:01, 10 September 2016

Crystal structure of PTK6 kinase domain

Structural highlights

5d7v is a 4 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Activity:	Non-specific protein-tyrosine kinase, with EC number 2.7.10.2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PTK6_HUMAN] Non-receptor tyrosine-protein kinase implicated in the regulation of a variety of signaling pathways that control the differentiation and maintenance of normal epithelia, as well as tumor growth. Function seems to be context dependent and differ depending on cell type, as well as its intracellular localization. A number of potential nuclear and cytoplasmic substrates have been identified. These include the RNA-binding proteins: KHDRBS1/SAM68, KHDRBS2/SLM1, KHDRBS3/SLM2 and SFPQ/PSF; transcription factors: STAT3 and STAT5A/B and a variety of signaling molecules: ARHGAP35/p190RhoGAP, PXN/paxillin, BTK/ATK, STAP2/BKS. Associates also with a variety of proteins that are likely upstream of PTK6 in various signaling pathways, or for which PTK6 may play an adapter-like role. These proteins include ADAM15, EGFR, ERBB2, ERBB3 and IRS4. In normal or non-tumorigenic tissues, PTK6 promotes cellular differentiation and apoptosis. In tumors PTK6 contributes to cancer progression by sensitizing cells to mitogenic signals and enhancing proliferation, anchorage-independent survival and migration/invasion. Association with EGFR, ERBB2, ERBB3 may contribute to mammary tumor development and growth through enhancement of EGF-induced signaling via BTK/AKT and PI3 kinase. Contributes to migration and proliferation by contributing to EGF-mediated phosphorylation of ARHGAP35/p190RhoGAP, which promotes association with RASA1/p120RasGAP, inactivating RhoA while activating RAS. EGF stimulation resulted in phosphorylation of PNX/Paxillin by PTK6 and activation of RAC1 via CRK/CrKII, thereby promoting migration and invasion. PTK6 activates STAT3 and STAT5B to promote proliferation. Nuclear PTK6 may be important for regulating growth in normal epithelia, while cytoplasmic PTK6 might activate oncogenic signaling pathways.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] Isoform 2 inhibits PTK6 phosphorylation and PTK6 association with other tyrosine-phosphorylated proteins.^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18]

Publication Abstract from PubMed

Human Protein tyrosine kinase 6 (PTK6) (EC:2.7.10.2), also known as the breast tumor kinase (BRK), is an intracellular non-receptor Src-related tyrosine kinase expressed in a majority of human breast tumors and breast cancer cell lines, but its expression is low or completely absent in normal mammary glands. In the recent past, several studies have suggested that PTK6 is a potential therapeutic target in cancer. To understand its structural and functional properties, the PTK6 kinase domain (PTK6-KD) gene was cloned, overexpressed in a baculo-insect cell system, purified and crystallized at room temperature. X-ray diffraction data to 2.33 A resolution was collected on a single PTK6-KD crystal, which belonged to the triclinic space group P1. The Matthews coefficient calculation suggested the presence of four protein molecules per asymmetric unit, with a solvent content of approximately 50%.The structure has been solved by molecular replacement and crystal structure data submitted to the protein data bank under the accession number 5D7V. This is the first report of apo PTK6-KD structure crystallized in DFG-in and alphaC-helix-out conformation.

Crystal structure of the kinase domain of human protein tyrosine kinase 6 (PTK6) at 2.33 A resolution.,Thakur MK, Kumar A, Birudukota S, Swaminathan S, Tyagi R, Gosu R Biochem Biophys Res Commun. 2016 Sep 16;478(2):637-42. doi:, 10.1016/j.bbrc.2016.07.121. Epub 2016 Jul 30. PMID:27480927^[19]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Mitchell PJ, Sara EA, Crompton MR. A novel adaptor-like protein which is a substrate for the non-receptor tyrosine kinase, BRK. Oncogene. 2000 Aug 31;19(37):4273-82. PMID:10980601 doi:http://dx.doi.org/10.1038/sj.onc.1203775
↑ Haegebarth A, Heap D, Bie W, Derry JJ, Richard S, Tyner AL. The nuclear tyrosine kinase BRK/Sik phosphorylates and inhibits the RNA-binding activities of the Sam68-like mammalian proteins SLM-1 and SLM-2. J Biol Chem. 2004 Dec 24;279(52):54398-404. Epub 2004 Oct 7. PMID:15471878 doi:http://dx.doi.org/10.1074/jbc.M409579200
↑ Chen HY, Shen CH, Tsai YT, Lin FC, Huang YP, Chen RH. Brk activates rac1 and promotes cell migration and invasion by phosphorylating paxillin. Mol Cell Biol. 2004 Dec;24(24):10558-72. PMID:15572663 doi:http://dx.doi.org/10.1128/MCB.24.24.10558-10572.2004
↑ Zhang P, Ostrander JH, Faivre EJ, Olsen A, Fitzsimmons D, Lange CA. Regulated association of protein kinase B/Akt with breast tumor kinase. J Biol Chem. 2005 Jan 21;280(3):1982-91. Epub 2004 Nov 10. PMID:15539407 doi:http://dx.doi.org/10.1074/jbc.M412038200
↑ Lukong KE, Larocque D, Tyner AL, Richard S. Tyrosine phosphorylation of sam68 by breast tumor kinase regulates intranuclear localization and cell cycle progression. J Biol Chem. 2005 Nov 18;280(46):38639-47. Epub 2005 Sep 22. PMID:16179349 doi:http://dx.doi.org/10.1074/jbc.M505802200
↑ Liu L, Gao Y, Qiu H, Miller WT, Poli V, Reich NC. Identification of STAT3 as a specific substrate of breast tumor kinase. Oncogene. 2006 Aug 10;25(35):4904-12. Epub 2006 Mar 27. PMID:16568091 doi:http://dx.doi.org/10.1038/sj.onc.1209501
↑ Weaver AM, Silva CM. Signal transducer and activator of transcription 5b: a new target of breast tumor kinase/protein tyrosine kinase 6. Breast Cancer Res. 2007;9(6):R79. PMID:17997837 doi:http://dx.doi.org/10.1186/bcr1794
↑ Shen CH, Chen HY, Lin MS, Li FY, Chang CC, Kuo ML, Settleman J, Chen RH. Breast tumor kinase phosphorylates p190RhoGAP to regulate rho and ras and promote breast carcinoma growth, migration, and invasion. Cancer Res. 2008 Oct 1;68(19):7779-87. doi: 10.1158/0008-5472.CAN-08-0997. PMID:18829532 doi:http://dx.doi.org/10.1158/0008-5472.CAN-08-0997
↑ Brauer PM, Zheng Y, Evans MD, Dominguez-Brauer C, Peehl DM, Tyner AL. The alternative splice variant of protein tyrosine kinase 6 negatively regulates growth and enhances PTK6-mediated inhibition of beta-catenin. PLoS One. 2011 Mar 30;6(3):e14789. doi: 10.1371/journal.pone.0014789. PMID:21479203 doi:http://dx.doi.org/10.1371/journal.pone.0014789
↑ Mitchell PJ, Sara EA, Crompton MR. A novel adaptor-like protein which is a substrate for the non-receptor tyrosine kinase, BRK. Oncogene. 2000 Aug 31;19(37):4273-82. PMID:10980601 doi:http://dx.doi.org/10.1038/sj.onc.1203775
↑ Haegebarth A, Heap D, Bie W, Derry JJ, Richard S, Tyner AL. The nuclear tyrosine kinase BRK/Sik phosphorylates and inhibits the RNA-binding activities of the Sam68-like mammalian proteins SLM-1 and SLM-2. J Biol Chem. 2004 Dec 24;279(52):54398-404. Epub 2004 Oct 7. PMID:15471878 doi:http://dx.doi.org/10.1074/jbc.M409579200
↑ Chen HY, Shen CH, Tsai YT, Lin FC, Huang YP, Chen RH. Brk activates rac1 and promotes cell migration and invasion by phosphorylating paxillin. Mol Cell Biol. 2004 Dec;24(24):10558-72. PMID:15572663 doi:http://dx.doi.org/10.1128/MCB.24.24.10558-10572.2004
↑ Zhang P, Ostrander JH, Faivre EJ, Olsen A, Fitzsimmons D, Lange CA. Regulated association of protein kinase B/Akt with breast tumor kinase. J Biol Chem. 2005 Jan 21;280(3):1982-91. Epub 2004 Nov 10. PMID:15539407 doi:http://dx.doi.org/10.1074/jbc.M412038200
↑ Lukong KE, Larocque D, Tyner AL, Richard S. Tyrosine phosphorylation of sam68 by breast tumor kinase regulates intranuclear localization and cell cycle progression. J Biol Chem. 2005 Nov 18;280(46):38639-47. Epub 2005 Sep 22. PMID:16179349 doi:http://dx.doi.org/10.1074/jbc.M505802200
↑ Liu L, Gao Y, Qiu H, Miller WT, Poli V, Reich NC. Identification of STAT3 as a specific substrate of breast tumor kinase. Oncogene. 2006 Aug 10;25(35):4904-12. Epub 2006 Mar 27. PMID:16568091 doi:http://dx.doi.org/10.1038/sj.onc.1209501
↑ Weaver AM, Silva CM. Signal transducer and activator of transcription 5b: a new target of breast tumor kinase/protein tyrosine kinase 6. Breast Cancer Res. 2007;9(6):R79. PMID:17997837 doi:http://dx.doi.org/10.1186/bcr1794
↑ Shen CH, Chen HY, Lin MS, Li FY, Chang CC, Kuo ML, Settleman J, Chen RH. Breast tumor kinase phosphorylates p190RhoGAP to regulate rho and ras and promote breast carcinoma growth, migration, and invasion. Cancer Res. 2008 Oct 1;68(19):7779-87. doi: 10.1158/0008-5472.CAN-08-0997. PMID:18829532 doi:http://dx.doi.org/10.1158/0008-5472.CAN-08-0997
↑ Brauer PM, Zheng Y, Evans MD, Dominguez-Brauer C, Peehl DM, Tyner AL. The alternative splice variant of protein tyrosine kinase 6 negatively regulates growth and enhances PTK6-mediated inhibition of beta-catenin. PLoS One. 2011 Mar 30;6(3):e14789. doi: 10.1371/journal.pone.0014789. PMID:21479203 doi:http://dx.doi.org/10.1371/journal.pone.0014789
↑ Thakur MK, Kumar A, Birudukota S, Swaminathan S, Tyagi R, Gosu R. Crystal structure of the kinase domain of human protein tyrosine kinase 6 (PTK6) at 2.33 A resolution. Biochem Biophys Res Commun. 2016 Sep 16;478(2):637-42. doi:, 10.1016/j.bbrc.2016.07.121. Epub 2016 Jul 30. PMID:27480927 doi:http://dx.doi.org/10.1016/j.bbrc.2016.07.121

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5d7v"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5d7v is ON HOLD  until Aug 14 2017
+==Crystal structure of PTK6 kinase domain==
+<StructureSection load='5d7v' size='340' side='right' caption='[[5d7v]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5d7v]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D7V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D7V FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_protein-tyrosine_kinase Non-specific protein-tyrosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.10.2 2.7.10.2] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5d7v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d7v OCA], [http://pdbe.org/5d7v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d7v RCSB], [http://www.ebi.ac.uk/pdbsum/5d7v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d7v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/PTK6_HUMAN PTK6_HUMAN]] Non-receptor tyrosine-protein kinase implicated in the regulation of a variety of signaling pathways that control the differentiation and maintenance of normal epithelia, as well as tumor growth. Function seems to be context dependent and differ depending on cell type, as well as its intracellular localization. A number of potential nuclear and cytoplasmic substrates have been identified. These include the RNA-binding proteins: KHDRBS1/SAM68, KHDRBS2/SLM1, KHDRBS3/SLM2 and SFPQ/PSF; transcription factors: STAT3 and STAT5A/B and a variety of signaling molecules: ARHGAP35/p190RhoGAP, PXN/paxillin, BTK/ATK, STAP2/BKS. Associates also with a variety of proteins that are likely upstream of PTK6 in various signaling pathways, or for which PTK6 may play an adapter-like role. These proteins include ADAM15, EGFR, ERBB2, ERBB3 and IRS4. In normal or non-tumorigenic tissues, PTK6 promotes cellular differentiation and apoptosis. In tumors PTK6 contributes to cancer progression by sensitizing cells to mitogenic signals and enhancing proliferation, anchorage-independent survival and migration/invasion. Association with EGFR, ERBB2, ERBB3 may contribute to mammary tumor development and growth through enhancement of EGF-induced signaling via BTK/AKT and PI3 kinase. Contributes to migration and proliferation by contributing to EGF-mediated phosphorylation of ARHGAP35/p190RhoGAP, which promotes association with RASA1/p120RasGAP, inactivating RhoA while activating RAS. EGF stimulation resulted in phosphorylation of PNX/Paxillin by PTK6 and activation of RAC1 via CRK/CrKII, thereby promoting migration and invasion. PTK6 activates STAT3 and STAT5B to promote proliferation. Nuclear PTK6 may be important for regulating growth in normal epithelia, while cytoplasmic PTK6 might activate oncogenic signaling pathways.<ref>PMID:10980601</ref> <ref>PMID:15471878</ref> <ref>PMID:15572663</ref> <ref>PMID:15539407</ref> <ref>PMID:16179349</ref> <ref>PMID:16568091</ref> <ref>PMID:17997837</ref> <ref>PMID:18829532</ref> <ref>PMID:21479203</ref>   Isoform 2 inhibits PTK6 phosphorylation and PTK6 association with other tyrosine-phosphorylated proteins.<ref>PMID:10980601</ref> <ref>PMID:15471878</ref> <ref>PMID:15572663</ref> <ref>PMID:15539407</ref> <ref>PMID:16179349</ref> <ref>PMID:16568091</ref> <ref>PMID:17997837</ref> <ref>PMID:18829532</ref> <ref>PMID:21479203</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human Protein tyrosine kinase 6 (PTK6) (EC:2.7.10.2), also known as the breast tumor kinase (BRK), is an intracellular non-receptor Src-related tyrosine kinase expressed in a majority of human breast tumors and breast cancer cell lines, but its expression is low or completely absent in normal mammary glands. In the recent past, several studies have suggested that PTK6 is a potential therapeutic target in cancer. To understand its structural and functional properties, the PTK6 kinase domain (PTK6-KD) gene was cloned, overexpressed in a baculo-insect cell system, purified and crystallized at room temperature. X-ray diffraction data to 2.33 A resolution was collected on a single PTK6-KD crystal, which belonged to the triclinic space group P1. The Matthews coefficient calculation suggested the presence of four protein molecules per asymmetric unit, with a solvent content of approximately 50%.The structure has been solved by molecular replacement and crystal structure data submitted to the protein data bank under the accession number 5D7V. This is the first report of apo PTK6-KD structure crystallized in DFG-in and alphaC-helix-out conformation.
-Authors:
+Crystal structure of the kinase domain of human protein tyrosine kinase 6 (PTK6) at 2.33 A resolution.,Thakur MK, Kumar A, Birudukota S, Swaminathan S, Tyagi R, Gosu R Biochem Biophys Res Commun. 2016 Sep 16;478(2):637-42. doi:, 10.1016/j.bbrc.2016.07.121. Epub 2016 Jul 30. PMID:27480927<ref>PMID:27480927</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5d7v" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Non-specific protein-tyrosine kinase]]
+[[Category: Birudukota, S]]
+[[Category: Gosu, R]]
+[[Category: Swaminathan, S]]
+[[Category: Thakur, M K]]
+[[Category: Tyagi, R]]
+[[Category: Apo]]
+[[Category: Brk]]
+[[Category: Kinase]]
+[[Category: Transferase]]

5d7v

From Proteopedia

Revision as of 00:01, 10 September 2016

Crystal structure of PTK6 kinase domain

Structural highlights

Function

Publication Abstract from PubMed

References

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Proteopedia Page Contributors and Editors (what is this?)

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