3bjf: Difference between revisions

Latest revision as of 09:29, 21 February 2024

Pyruvate kinase M2 is a phosphotyrosine binding protein

Structural highlights

3bjf 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:	X-ray diffraction, Resolution 2.03Å
Ligands:	FBP, K, MG, OXL
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]

Evolutionary Conservation

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

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

Proteopedia Page Contributors and Editors (what is this?)

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

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-[[Image:3bjf.jpg|left|200px]]<br /><applet load="3bjf" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="3bjf, resolution 2.03&Aring;" />
-'''Pyruvate kinase M2 is a phosphotyrosine binding protein'''<br />
-==About this Structure==
+==Pyruvate kinase M2 is a phosphotyrosine binding protein==
-BJF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=FBP:'>FBP</scene>, <scene name='pdbligand=OXL:'>OXL</scene>, <scene name='pdbligand=K:'>K</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Sites: <scene name='pdbsite=AC1:Fbp+Binding+Site+For+Residue+A+532'>AC1</scene>, <scene name='pdbsite=AC2:Fbp+Binding+Site+For+Residue+B+532'>AC2</scene>, <scene name='pdbsite=AC3:Fbp+Binding+Site+For+Residue+C+532'>AC3</scene>, <scene name='pdbsite=AC4:Fbp+Binding+Site+For+Residue+D+532'>AC4</scene>, <scene name='pdbsite=AC5:Oxl+Binding+Site+For+Residue+A+901'>AC5</scene>, <scene name='pdbsite=AC6:Oxl+Binding+Site+For+Residue+B+902'>AC6</scene>, <scene name='pdbsite=AC7:Oxl+Binding+Site+For+Residue+C+903'>AC7</scene>, <scene name='pdbsite=AC8:Oxl+Binding+Site+For+Residue+D+904'>AC8</scene>, <scene name='pdbsite=AC9:K+Binding+Site+For+Residue+A+601'>AC9</scene>, <scene name='pdbsite=BC1:K+Binding+Site+For+Residue+B+602'>BC1</scene>, <scene name='pdbsite=BC2:K+Binding+Site+For+Residue+C+603'>BC2</scene>, <scene name='pdbsite=BC3:K+Binding+Site+For+Residue+D+604'>BC3</scene>, <scene name='pdbsite=BC4:Mg+Binding+Site+For+Residue+A+701'>BC4</scene>, <scene name='pdbsite=BC5:Mg+Binding+Site+For+Residue+B+702'>BC5</scene>, <scene name='pdbsite=BC6:Mg+Binding+Site+For+Residue+C+703'>BC6</scene> and <scene name='pdbsite=BC7:Mg+Binding+Site+For+Residue+D+704'>BC7</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BJF OCA].
+<StructureSection load='3bjf' size='340' side='right'caption='[[3bjf]], [[Resolution|resolution]] 2.03&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3bjf]] 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=3BJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BJF FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.03&#8491;</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene></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=3bjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bjf OCA], [https://pdbe.org/3bjf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bjf RCSB], [https://www.ebi.ac.uk/pdbsum/3bjf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bjf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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>
+== 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/bj/3bjf_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3bjf ConSurf].
+<div style="clear:both"></div>
+==See Also==
+*[[Pyruvate kinase 3D structures|Pyruvate kinase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Pyruvate kinase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Wu N]]
-[[Category: Wu, N.]]
-[[Category: FBP]]
-[[Category: K]]
-[[Category: MG]]
-[[Category: OXL]]
-[[Category: acetylation]]
-[[Category: allosteric enzyme]]
-[[Category: alternative splicing]]
-[[Category: glycolysis]]
-[[Category: magnesium]]
-[[Category: metal-binding]]
-[[Category: phosphoprotein]]
-[[Category: polymorphism]]
-[[Category: pyruvate kinase]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar  5 13:23:55 2008''

3bjf: Difference between revisions

Latest revision as of 09:29, 21 February 2024

Pyruvate kinase M2 is a phosphotyrosine binding protein

Structural highlights

Function

Evolutionary Conservation

See Also

References

Contents

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