2uw3: Difference between revisions

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{{Seed}}
[[Image:2uw3.png|left|200px]]


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==Structure of PKA-PKB chimera complexed with 5-methyl-4-phenyl-1H- pyrazole==
The line below this paragraph, containing "STRUCTURE_2uw3", creates the "Structure Box" on the page.
<StructureSection load='2uw3' size='340' side='right'caption='[[2uw3]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2uw3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UW3 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.19&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GVG:3-METHYL-4-PHENYL-1H-PYRAZOLE'>GVG</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
{{STRUCTURE_2uw3| PDB=2uw3 |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2uw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uw3 OCA], [https://pdbe.org/2uw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uw3 RCSB], [https://www.ebi.ac.uk/pdbsum/2uw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uw3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KAPCA_BOVIN KAPCA_BOVIN] Phosphorylates a large number of substrates in the cytoplasm and the nucleus. Regulates the abundance of compartmentalized pools of its regulatory subunits through phosphorylation of PJA2 which binds and ubiquitinates these subunits, leading to their subsequent proteolysis. Phosphorylates CDC25B, ABL1, NFKB1, CLDN3, PSMC5/RPT6, PJA2, RYR2, RORA, TRPC1 and VASP. RORA is activated by phosphorylation. Required for glucose-mediated adipogenic differentiation increase and osteogenic differentiation inhibition from osteoblasts. Involved in the regulation of platelets in response to thrombin and collagen; maintains circulating platelets in a resting state by phosphorylating proteins in numerous platelet inhibitory pathways when in complex with NF-kappa-B (NFKB1 and NFKB2) and I-kappa-B-alpha (NFKBIA), but thrombin and collagen disrupt these complexes and free active PRKACA stimulates platelets and leads to platelet aggregation by phosphorylating VASP. Prevents the antiproliferative and anti-invasive effects of alpha-difluoromethylornithine in breast cancer cells when activated. RYR2 channel activity is potentiated by phosphorylation in presence of luminal Ca(2+), leading to reduced amplitude and increased frequency of store overload-induced Ca(2+) release (SOICR) characterized by an increased rate of Ca(2+) release and propagation velocity of spontaneous Ca(2+) waves, despite reduced wave amplitude and resting cytosolic Ca(2+). TRPC1 activation by phosphorylation promotes Ca(2+) influx, essential for the increase in permeability induced by thrombin in confluent endothelial monolayers. PSMC5/RPT6 activation by phosphorylation stimulates proteasome. Regulates negatively tight junction (TJs) in ovarian cancer cells via CLDN3 phosphorylation. NFKB1 phosphorylation promotes NF-kappa-B p50-p50 DNA binding. Involved in embryonic development by down-regulating the Hedgehog (Hh) signaling pathway that determines embryo pattern formation and morphogenesis. Isoform 2 phosphorylates and activates ABL1 in sperm flagellum to promote spermatozoa capacitation. Prevents meiosis resumption in prophase-arrested oocytes via CDC25B inactivation by phosphorylation. May also regulate rapid eye movement (REM) sleep in the pedunculopontine tegmental (PPT) (By similarity).
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uw/2uw3_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2uw3 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Using fragment-based screening techniques, 5-methyl-4-phenyl-1H-pyrazole (IC50 80 microM) was identified as a novel, low molecular weight inhibitor of protein kinase B (PKB). Herein we describe the rapid elaboration of highly potent and ligand efficient analogues using a fragment growing approach. Iterative structure-based design was supported by protein-ligand structure determinations using a PKA-PKB "chimera" and a final protein-ligand structure of a lead compound in PKBbeta itself.


===STRUCTURE OF PKA-PKB CHIMERA COMPLEXED WITH 5-METHYL-4-PHENYL-1H-PYRAZOLE===
Identification of inhibitors of protein kinase B using fragment-based lead discovery.,Saxty G, Woodhead SJ, Berdini V, Davies TG, Verdonk ML, Wyatt PG, Boyle RG, Barford D, Downham R, Garrett MD, Carr RA J Med Chem. 2007 May 17;50(10):2293-6. Epub 2007 Apr 24. PMID:17451234<ref>PMID:17451234</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2uw3" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17451234}}, adds the Publication Abstract to the page
*[[CAMP-dependent protein kinase 3D structures|CAMP-dependent protein kinase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17451234 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_17451234}}
__TOC__
 
</StructureSection>
==About this Structure==
2UW3 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UW3 OCA].
 
==Reference==
Identification of inhibitors of protein kinase B using fragment-based lead discovery., Saxty G, Woodhead SJ, Berdini V, Davies TG, Verdonk ML, Wyatt PG, Boyle RG, Barford D, Downham R, Garrett MD, Carr RA, J Med Chem. 2007 May 17;50(10):2293-6. Epub 2007 Apr 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17451234 17451234]
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Protein complex]]
[[Category: Homo sapiens]]
[[Category: CAMP-dependent protein kinase]]
[[Category: Large Structures]]
[[Category: Barford, D.]]
[[Category: Barford D]]
[[Category: Berdini, V.]]
[[Category: Berdini V]]
[[Category: Boyle, R G.]]
[[Category: Boyle RG]]
[[Category: Carr, R A.]]
[[Category: Carr RA]]
[[Category: Davies, T G.]]
[[Category: Davies TG]]
[[Category: Downham, R.]]
[[Category: Downham R]]
[[Category: Garrett, M D.]]
[[Category: Garrett MD]]
[[Category: Saxty, G.]]
[[Category: Saxty G]]
[[Category: Verdonk, M L.]]
[[Category: Verdonk ML]]
[[Category: Woodhead, S J.]]
[[Category: Woodhead SJ]]
[[Category: Wyatt, P G.]]
[[Category: Wyatt PG]]
[[Category: Atp-binding]]
[[Category: Camp]]
[[Category: Kinase]]
[[Category: Lipoprotein]]
[[Category: Myristate]]
[[Category: Nuclear protein]]
[[Category: Nucleotide-binding]]
[[Category: Phosphorylation]]
[[Category: Protein kinase inhibitor]]
[[Category: Serine/threonine-protein kinase]]
[[Category: Transferase]]
[[Category: Transferase/inhibitor complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 01:11:54 2008''

Latest revision as of 12:30, 6 November 2024

Structure of PKA-PKB chimera complexed with 5-methyl-4-phenyl-1H- pyrazoleStructure of PKA-PKB chimera complexed with 5-methyl-4-phenyl-1H- pyrazole

Structural highlights

2uw3 is a 2 chain structure with sequence from Bos taurus and Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.19Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KAPCA_BOVIN Phosphorylates a large number of substrates in the cytoplasm and the nucleus. Regulates the abundance of compartmentalized pools of its regulatory subunits through phosphorylation of PJA2 which binds and ubiquitinates these subunits, leading to their subsequent proteolysis. Phosphorylates CDC25B, ABL1, NFKB1, CLDN3, PSMC5/RPT6, PJA2, RYR2, RORA, TRPC1 and VASP. RORA is activated by phosphorylation. Required for glucose-mediated adipogenic differentiation increase and osteogenic differentiation inhibition from osteoblasts. Involved in the regulation of platelets in response to thrombin and collagen; maintains circulating platelets in a resting state by phosphorylating proteins in numerous platelet inhibitory pathways when in complex with NF-kappa-B (NFKB1 and NFKB2) and I-kappa-B-alpha (NFKBIA), but thrombin and collagen disrupt these complexes and free active PRKACA stimulates platelets and leads to platelet aggregation by phosphorylating VASP. Prevents the antiproliferative and anti-invasive effects of alpha-difluoromethylornithine in breast cancer cells when activated. RYR2 channel activity is potentiated by phosphorylation in presence of luminal Ca(2+), leading to reduced amplitude and increased frequency of store overload-induced Ca(2+) release (SOICR) characterized by an increased rate of Ca(2+) release and propagation velocity of spontaneous Ca(2+) waves, despite reduced wave amplitude and resting cytosolic Ca(2+). TRPC1 activation by phosphorylation promotes Ca(2+) influx, essential for the increase in permeability induced by thrombin in confluent endothelial monolayers. PSMC5/RPT6 activation by phosphorylation stimulates proteasome. Regulates negatively tight junction (TJs) in ovarian cancer cells via CLDN3 phosphorylation. NFKB1 phosphorylation promotes NF-kappa-B p50-p50 DNA binding. Involved in embryonic development by down-regulating the Hedgehog (Hh) signaling pathway that determines embryo pattern formation and morphogenesis. Isoform 2 phosphorylates and activates ABL1 in sperm flagellum to promote spermatozoa capacitation. Prevents meiosis resumption in prophase-arrested oocytes via CDC25B inactivation by phosphorylation. May also regulate rapid eye movement (REM) sleep in the pedunculopontine tegmental (PPT) (By similarity).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Using fragment-based screening techniques, 5-methyl-4-phenyl-1H-pyrazole (IC50 80 microM) was identified as a novel, low molecular weight inhibitor of protein kinase B (PKB). Herein we describe the rapid elaboration of highly potent and ligand efficient analogues using a fragment growing approach. Iterative structure-based design was supported by protein-ligand structure determinations using a PKA-PKB "chimera" and a final protein-ligand structure of a lead compound in PKBbeta itself.

Identification of inhibitors of protein kinase B using fragment-based lead discovery.,Saxty G, Woodhead SJ, Berdini V, Davies TG, Verdonk ML, Wyatt PG, Boyle RG, Barford D, Downham R, Garrett MD, Carr RA J Med Chem. 2007 May 17;50(10):2293-6. Epub 2007 Apr 24. PMID:17451234[1]

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

See Also

References

  1. Saxty G, Woodhead SJ, Berdini V, Davies TG, Verdonk ML, Wyatt PG, Boyle RG, Barford D, Downham R, Garrett MD, Carr RA. Identification of inhibitors of protein kinase B using fragment-based lead discovery. J Med Chem. 2007 May 17;50(10):2293-6. Epub 2007 Apr 24. PMID:17451234 doi:10.1021/jm070091b

2uw3, resolution 2.19Å

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