6ttq: Difference between revisions

Latest revision as of 13:19, 22 May 2024

PKM2 in complex with Compound 10PKM2 in complex with Compound 10

6ttq, resolution 2.70Å

Structural highlights

6ttq is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.7Å
Ligands:
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

KPYM_HUMAN Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Recent advances in cryo-electron microscopy (EM) structure determination have pushed the resolutions obtainable by the method into the range widely considered to be of utility for drug discovery. Here, we review the use of cryo-EM in fragment-based drug discovery (FBDD) based on in-house method development. We demonstrate not only that cryo-EM can reveal details of the molecular interactions between fragments and a protein, but also that the current reproducibility, quality, and throughput are compatible with FBDD. We exemplify this using the test system beta-galactosidase (Bgal) and the oncology target pyruvate kinase 2 (PKM2).

Fragment-based drug discovery using cryo-EM.,Saur M, Hartshorn MJ, Dong J, Reeks J, Bunkoczi G, Jhoti H, Williams PA Drug Discov Today. 2019 Dec 23. pii: S1359-6446(19)30465-9. doi:, 10.1016/j.drudis.2019.12.006. PMID:31877353^[4]

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

References

↑ Stetak A, Veress R, Ovadi J, Csermely P, Keri G, Ullrich A. Nuclear translocation of the tumor marker pyruvate kinase M2 induces programmed cell death. Cancer Res. 2007 Feb 15;67(4):1602-8. PMID:17308100 doi:10.1158/0008-5472.CAN-06-2870
↑ Lee J, Kim HK, Han YM, Kim J. Pyruvate kinase isozyme type M2 (PKM2) interacts and cooperates with Oct-4 in regulating transcription. Int J Biochem Cell Biol. 2008;40(5):1043-54. doi: 10.1016/j.biocel.2007.11.009., Epub 2007 Nov 29. PMID:18191611 doi:10.1016/j.biocel.2007.11.009
↑ Luo W, Hu H, Chang R, Zhong J, Knabel M, O'Meally R, Cole RN, Pandey A, Semenza GL. Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1. Cell. 2011 May 27;145(5):732-44. doi: 10.1016/j.cell.2011.03.054. PMID:21620138 doi:10.1016/j.cell.2011.03.054
↑ Saur M, Hartshorn MJ, Dong J, Reeks J, Bunkoczi G, Jhoti H, Williams PA. Fragment-based drug discovery using cryo-EM. Drug Discov Today. 2019 Dec 23. pii: S1359-6446(19)30465-9. doi:, 10.1016/j.drudis.2019.12.006. PMID:31877353 doi:http://dx.doi.org/10.1016/j.drudis.2019.12.006

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OCA

[1] Stetak A, Veress R, Ovadi J, Csermely P, Keri G, Ullrich A. Nuclear translocation of the tumor marker pyruvate kinase M2 induces programmed cell death. Cancer Res. 2007 Feb 15;67(4):1602-8. PMID:17308100 doi:10.1158/0008-5472.CAN-06-2870

[2] Lee J, Kim HK, Han YM, Kim J. Pyruvate kinase isozyme type M2 (PKM2) interacts and cooperates with Oct-4 in regulating transcription. Int J Biochem Cell Biol. 2008;40(5):1043-54. doi: 10.1016/j.biocel.2007.11.009., Epub 2007 Nov 29. PMID:18191611 doi:10.1016/j.biocel.2007.11.009

[3] Luo W, Hu H, Chang R, Zhong J, Knabel M, O'Meally R, Cole RN, Pandey A, Semenza GL. Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1. Cell. 2011 May 27;145(5):732-44. doi: 10.1016/j.cell.2011.03.054. PMID:21620138 doi:10.1016/j.cell.2011.03.054

[4] Saur M, Hartshorn MJ, Dong J, Reeks J, Bunkoczi G, Jhoti H, Williams PA. Fragment-based drug discovery using cryo-EM. Drug Discov Today. 2019 Dec 23. pii: S1359-6446(19)30465-9. doi:, 10.1016/j.drudis.2019.12.006. PMID:31877353 doi:http://dx.doi.org/10.1016/j.drudis.2019.12.006

[1]

[2]

[3]

[4]

@@ Line 3: / Line 3: @@
 <SX load='6ttq' size='340' side='right' viewer='molstar' caption='[[6ttq]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ttq]] is a 4 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=6TTQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TTQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ttq]] is a 4 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=6TTQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TTQ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NXH:1-propan-2-yl-3-pyridin-4-yl-urea'>NXH</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PKM, OIP3, PK2, PK3, PKM2 ([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=FBP:BETA-FRUCTOSE-1,6-DIPHOSPHATE'>FBP</scene>, <scene name='pdbligand=NXH:1-propan-2-yl-3-pyridin-4-yl-urea'>NXH</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_kinase Pyruvate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.40 2.7.1.40] </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=6ttq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ttq OCA], [https://pdbe.org/6ttq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ttq RCSB], [https://www.ebi.ac.uk/pdbsum/6ttq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ttq ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ttq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ttq OCA], [http://pdbe.org/6ttq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ttq RCSB], [http://www.ebi.ac.uk/pdbsum/6ttq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ttq ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KPYM_HUMAN KPYM_HUMAN]] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.<ref>PMID:17308100</ref> <ref>PMID:18191611</ref> <ref>PMID:21620138</ref>
+[https://www.uniprot.org/uniprot/KPYM_HUMAN KPYM_HUMAN] Glycolytic enzyme that catalyzes the transfer of a phosphoryl group from phosphoenolpyruvate (PEP) to ADP, generating ATP. Stimulates POU5F1-mediated transcriptional activation. Plays a general role in caspase independent cell death of tumor cells. The ratio betwween the highly active tetrameric form and nearly inactive dimeric form determines whether glucose carbons are channeled to biosynthetic processes or used for glycolytic ATP production. The transition between the 2 forms contributes to the control of glycolysis and is important for tumor cell proliferation and survival.<ref>PMID:17308100</ref> <ref>PMID:18191611</ref> <ref>PMID:21620138</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 6ttq" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Pyruvate kinase 3D structures|Pyruvate kinase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </SX>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Pyruvate kinase]]
+[[Category: Bunkoczi G]]
-[[Category: Bunkoczi, G]]
+[[Category: Dong J]]
-[[Category: Dong, J]]
+[[Category: Hartshorn MJ]]
-[[Category: Hartshorn, M J]]
+[[Category: Jhoti H]]
-[[Category: Jhoti, H]]
+[[Category: Reeks J]]
-[[Category: Reeks, J]]
+[[Category: Saur M]]
-[[Category: Saur, M]]
+[[Category: Williams PA]]
-[[Category: Williams, P A]]
-[[Category: Cytosolic protein]]
-[[Category: Fbdd]]
-[[Category: Pkm2]]

6ttq: Difference between revisions

Latest revision as of 13:19, 22 May 2024

PKM2 in complex with Compound 10PKM2 in complex with Compound 10

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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6ttq: Difference between revisions

Latest revision as of 13:19, 22 May 2024

PKM2 in complex with Compound 10PKM2 in complex with Compound 10

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

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