6nfy - Revision history

OCA at 14:47, 13 March 2024

2024-03-13T14:47:35Z

←Older revision		Revision as of 14:47, 13 March 2024
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	<StructureSection load='6nfy' size='340' side='right'caption='[[6nfy]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='6nfy' size='340' side='right'caption='[[6nfy]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nfy]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NFY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NFY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nfy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NFY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B49:N-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>B49</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.17Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAP4K1, HPK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B49:N-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>B49</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_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6nfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfy OCA], [https://pdbe.org/6nfy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nfy RCSB], [https://www.ebi.ac.uk/pdbsum/6nfy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfy ProSAT]</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=6nfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfy OCA], [~~http~~://pdbe.org/6nfy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nfy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nfy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfy ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/M4K1_HUMAN M4K1_HUMAN]] Serine/threonine-protein kinase, which may play a role in the response to environmental stress. Appears to act upstream of the JUN N-terminal pathway. May play a role in hematopoietic lineage decisions and growth regulation. Able to autophosphorylate.<ref>PMID:24362026</ref> <ref>PMID:8824585</ref>	+	[https://www.uniprot.org/uniprot/M4K1_HUMAN M4K1_HUMAN] Serine/threonine-protein kinase, which may play a role in the response to environmental stress. Appears to act upstream of the JUN N-terminal pathway. May play a role in hematopoietic lineage decisions and growth regulation. Able to autophosphorylate.<ref>PMID:24362026</ref> <ref>PMID:8824585</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Hematopoietic progenitor kinase 1 (HPK1 or MAP4K1) is a Ser/Thr kinase that operates via the c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) signaling pathways, to dampen the T-cell response and antitumor immunity. Accordingly, selective HPK1 inhibition is considered a means to enhance antitumor immunity. Sunitinib, a multi-receptor tyrosine kinase (RTK) inhibitor approved for the management of gastrointestinal stromal tumors (GISTs), renal cell carcinoma (RCC), and pancreatic cancer, has been reported to inhibit HPK1 in vitro In this report we describe the crystal structures of the native HPK1 kinase domain in both nonphosphorylated and doubly phosphorylated states, in addition to a double phosphomimetic mutant (T165E, S171E), each complexed with sunitinib at 2.17-3.00 A resolutions. The native nonphosphorylated co-crystal structure revealed an inactive dimer in which the activation loop of each monomer partially occupies the ATP- and substrate-binding sites of the partner monomer. In contrast, the structure of the protein with a doubly phosphorylated activation loop exhibited an active kinase conformation with a greatly reduced monomer-monomer interface. On the other hand, the phosphomimetic mutant co-crystal structure disclosed an alternative arrangement in which the activation loops are in an extended domain-swapped configuration. These structural results indicate that HPK1 is a highly dynamic kinase that undergoes trans-regulation via dimer formation and extensive intramolecular and intermolecular remodeling of the activation segment.	+

-	Multiple conformational states of the HPK1 kinase domain in complex with sunitinib reveal the structural changes accompanying HPK1 trans-regulation.,Johnson E, McTigue M, Gallego RA, Johnson TW, Timofeevski S, Maestre M, Fisher TS, Kania R, Sawasdikosol S, Burakoff S, Cronin CN J Biol Chem. 2019 Apr 24. pii: AC119.007466. doi: 10.1074/jbc.AC119.007466. PMID:31018963<ref>PMID:31018963</ref>	+	==See Also==
-		+	*[[Mitogen-activated protein kinase kinase kinase\|Mitogen-activated protein kinase kinase kinase]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6nfy" style~~=~~"background~~-~~color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Non-specific serine/threonine protein kinase]]~~	+	[[Category: Cronin CN]]
-	[[Category: Cronin~~, C N~~]]	+	[[Category: Johnson E]]
-	[[Category: Johnson, E]]	+	[[Category: McTigue M]]
-	[[Category: McTigue, M]]	+
-	~~[[Category: 3d domain swap]]~~	+
-	~~[[Category: Active state]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 13:40, 10 May 2019

2019-05-10T13:40:57Z

←Older revision		Revision as of 13:40, 10 May 2019
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	<StructureSection load='6nfy' size='340' side='right'caption='[[6nfy]], [[Resolution\|resolution]] 2.17Å' scene=''>		<StructureSection load='6nfy' size='340' side='right'caption='[[6nfy]], [[Resolution\|resolution]] 2.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nfy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NFY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nfy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NFY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B49:N-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>B49</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B49:N-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>B49</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAP4K1, HPK1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </span></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_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=6nfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfy OCA], [http://pdbe.org/6nfy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nfy RCSB], [http://www.ebi.ac.uk/pdbsum/6nfy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfy ProSAT]</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=6nfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfy OCA], [http://pdbe.org/6nfy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nfy RCSB], [http://www.ebi.ac.uk/pdbsum/6nfy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfy ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/M4K1_HUMAN M4K1_HUMAN]] Serine/threonine-protein kinase, which may play a role in the response to environmental stress. Appears to act upstream of the JUN N-terminal pathway. May play a role in hematopoietic lineage decisions and growth regulation. Able to autophosphorylate.<ref>PMID:24362026</ref> <ref>PMID:8824585</ref>		[[http://www.uniprot.org/uniprot/M4K1_HUMAN M4K1_HUMAN]] Serine/threonine-protein kinase, which may play a role in the response to environmental stress. Appears to act upstream of the JUN N-terminal pathway. May play a role in hematopoietic lineage decisions and growth regulation. Able to autophosphorylate.<ref>PMID:24362026</ref> <ref>PMID:8824585</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Hematopoietic progenitor kinase 1 (HPK1 or MAP4K1) is a Ser/Thr kinase that operates via the c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK) signaling pathways, to dampen the T-cell response and antitumor immunity. Accordingly, selective HPK1 inhibition is considered a means to enhance antitumor immunity. Sunitinib, a multi-receptor tyrosine kinase (RTK) inhibitor approved for the management of gastrointestinal stromal tumors (GISTs), renal cell carcinoma (RCC), and pancreatic cancer, has been reported to inhibit HPK1 in vitro In this report we describe the crystal structures of the native HPK1 kinase domain in both nonphosphorylated and doubly phosphorylated states, in addition to a double phosphomimetic mutant (T165E, S171E), each complexed with sunitinib at 2.17-3.00 A resolutions. The native nonphosphorylated co-crystal structure revealed an inactive dimer in which the activation loop of each monomer partially occupies the ATP- and substrate-binding sites of the partner monomer. In contrast, the structure of the protein with a doubly phosphorylated activation loop exhibited an active kinase conformation with a greatly reduced monomer-monomer interface. On the other hand, the phosphomimetic mutant co-crystal structure disclosed an alternative arrangement in which the activation loops are in an extended domain-swapped configuration. These structural results indicate that HPK1 is a highly dynamic kinase that undergoes trans-regulation via dimer formation and extensive intramolecular and intermolecular remodeling of the activation segment.
		+
		+	Multiple conformational states of the HPK1 kinase domain in complex with sunitinib reveal the structural changes accompanying HPK1 trans-regulation.,Johnson E, McTigue M, Gallego RA, Johnson TW, Timofeevski S, Maestre M, Fisher TS, Kania R, Sawasdikosol S, Burakoff S, Cronin CN J Biol Chem. 2019 Apr 24. pii: AC119.007466. doi: 10.1074/jbc.AC119.007466. PMID:31018963<ref>PMID:31018963</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6nfy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Non-specific serine/threonine protein kinase]]		[[Category: Non-specific serine/threonine protein kinase]]

OCA at 08:54, 1 May 2019

2019-05-01T08:54:23Z

←Older revision		Revision as of 08:54, 1 May 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6nfy is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of nonphosphorylated, HPK1 kinase domain in complex with sunitinib in the inactive state.==
-		+	<StructureSection load='6nfy' size='340' side='right'caption='[[6nfy]], [[Resolution\|resolution]] 2.17Å' scene=''>
-	~~Authors~~: ~~Johnson~~, E., ~~McTigue~~, M., ~~Cronin~~, C.N.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6nfy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NFY FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of nonphosphorylated~~, ~~HPK1 kinase domain in complex with sunitinib~~ in the ~~inactive state~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B49:N-[2-(DIETHYLAMINO)ETHYL]-5-[(Z)-(5-FLUORO-2-OXO-1,2-DIHYDRO-3H-INDOL-3-YLIDENE)METHYL]-2,4-DIMETHYL-1H-PYRROLE-3-CARBOXAMIDE'>B49</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </span></td></tr>
-	[[Category: ~~Mctigue, M~~]]	+	<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=6nfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nfy OCA], [http://pdbe.org/6nfy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nfy RCSB], [http://www.ebi.ac.uk/pdbsum/6nfy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nfy ProSAT]</span></td></tr>
-	[[Category: Cronin, C.N]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/M4K1_HUMAN M4K1_HUMAN]] Serine/threonine-protein kinase, which may play a role in the response to environmental stress. Appears to act upstream of the JUN N-terminal pathway. May play a role in hematopoietic lineage decisions and growth regulation. Able to autophosphorylate.<ref>PMID:24362026</ref> <ref>PMID:8824585</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Non-specific serine/threonine protein kinase]]
		+	[[Category: Cronin, C N]]
	[[Category: Johnson, E]]		[[Category: Johnson, E]]
		+	[[Category: McTigue, M]]
		+	[[Category: 3d domain swap]]
		+	[[Category: Active state]]
		+	[[Category: Kinase]]
		+	[[Category: Transferase]]

OCA at 05:04, 21 February 2019

2019-02-21T05:04:08Z

←Older revision		Revision as of 05:04, 21 February 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6nfy is ON HOLD	+	The entry 6nfy is ON HOLD until Paper Publication

	Authors: Johnson, E., McTigue, M., Cronin, C.N.		Authors: Johnson, E., McTigue, M., Cronin, C.N.

OCA: Protected "6nfy" [edit=sysop:move=sysop]

2019-01-02T04:54:28Z

Protected "6nfy" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:54, 2 January 2019

OCA: New page: '''Unreleased structure''' The entry 6nfy is ON HOLD Authors: Johnson, E., McTigue, M., Cronin, C.N. Description: Crystal structure of nonphosphorylated, HPK1 kinase domain in complex ...

2019-01-02T04:54:27Z

New page: '''Unreleased structure''' The entry 6nfy is ON HOLD Authors: Johnson, E., McTigue, M., Cronin, C.N. Description: Crystal structure of nonphosphorylated, HPK1 kinase domain in complex ...

New page

'''Unreleased structure'''

The entry 6nfy is ON HOLD

Authors: Johnson, E., McTigue, M., Cronin, C.N.

Description: Crystal structure of nonphosphorylated, HPK1 kinase domain in complex with sunitinib in the inactive state.
[[Category: Unreleased Structures]]
[[Category: Mctigue, M]]
[[Category: Cronin, C.N]]
[[Category: Johnson, E]]