2p9t: Difference between revisions

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-[[Image:2p9t.jpg|left|200px]]
- {{Structure
+==Crystal Structure of Phosphoglycerate Kinase-2 bound to 3-phosphoglycerate==
-|PDB= 2p9t |SIZE=350|CAPTION= <scene name='initialview01'>2p9t</scene>, resolution 2.00&Aring;
+<StructureSection load='2p9t' size='340' side='right'caption='[[2p9t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=3PG:3-PHOSPHOGLYCERIC ACID'>3PG</scene>
+<table><tr><td colspan='2'>[[2p9t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P9T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P9T FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Phosphoglycerate_kinase Phosphoglycerate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.3 2.7.2.3]
+</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&#8491;</td></tr>
-|GENE= Pgk2, Pgk-2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PG:3-PHOSPHOGLYCERIC+ACID'>3PG</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=2p9t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p9t OCA], [https://pdbe.org/2p9t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p9t RCSB], [https://www.ebi.ac.uk/pdbsum/2p9t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p9t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PGK2_MOUSE PGK2_MOUSE]
+== 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/p9/2p9t_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=2p9t ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Phosphoglycerate kinase 2 (PGK2) is an isozyme of the glycolytic pathway that provides ATP required for sperm motility. It is encoded by an autosomal retrogene that is expressed only during spermatogenesis, concomitant with the inactivation of the X-linked Pgk1 gene. PGK2 from the mouse, Mus musculus, has been overexpressed from a plasmid in bacteria and purified. It was crystallized in three forms: as the apoenzyme, as a complex with 3-phosphoglycerate (3PG), and as a complex with 3PG and ATP. The crystal structures were solved to 2.7, 2.0, and 2.7 A resolutions, respectively. The overall fold is nearly identical with previously solved mammalian PGK1 molecules. The apoenzyme is in the "open" form; that is the N-terminal domain that can bind 3PG and the C-terminal domain that binds ATP are too far apart for the substrates to interact. Binding 3PG causes a 13 degrees rotation that partially closes the structure and causes helix 13, which is disordered in the unliganded structure, to stabilize. Binding ATP leaves the protein in the open configuration but also causes helix 13 to be ordered. Sequence alignment suggests that the active site of PGK2 is essentially identical to that of the cytoplasmic PGK1, but significant differences accumulate on a side of the C-terminal domain away from the active site. These changes may mediate the binding of this isoform to other proteins within the sperm flagellum, while still allowing the hinging action between the domains that is essential to catalytic activity. Proteins 2007. (c) 2007 Wiley-Liss, Inc.
-'''Crystal Structure of Phosphoglycerate Kinase-2 bound to 3-phosphoglycerate'''
+X-ray analysis of phosphoglycerate kinase 2, a sperm-specific isoform from Mus musculus.,Sawyer GM, Monzingo AF, Poteet EC, O'Brien DA, Robertus JD Proteins. 2007 Nov 14;. PMID:18004764<ref>PMID:18004764</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2p9t" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Phosphoglycerate kinase 2 (PGK2) is an isozyme of the glycolytic pathway that provides ATP required for sperm motility. It is encoded by an autosomal retrogene that is expressed only during spermatogenesis, concomitant with the inactivation of the X-linked Pgk1 gene. PGK2 from the mouse, Mus musculus, has been overexpressed from a plasmid in bacteria and purified. It was crystallized in three forms: as the apoenzyme, as a complex with 3-phosphoglycerate (3PG), and as a complex with 3PG and ATP. The crystal structures were solved to 2.7, 2.0, and 2.7 A resolutions, respectively. The overall fold is nearly identical with previously solved mammalian PGK1 molecules. The apoenzyme is in the "open" form; that is the N-terminal domain that can bind 3PG and the C-terminal domain that binds ATP are too far apart for the substrates to interact. Binding 3PG causes a 13 degrees rotation that partially closes the structure and causes helix 13, which is disordered in the unliganded structure, to stabilize. Binding ATP leaves the protein in the open configuration but also causes helix 13 to be ordered. Sequence alignment suggests that the active site of PGK2 is essentially identical to that of the cytoplasmic PGK1, but significant differences accumulate on a side of the C-terminal domain away from the active site. These changes may mediate the binding of this isoform to other proteins within the sperm flagellum, while still allowing the hinging action between the domains that is essential to catalytic activity. Proteins 2007. (c) 2007 Wiley-Liss, Inc.
+*[[Phosphoglycerate kinase 3D structures|Phosphoglycerate kinase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-P9T is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P9T OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-X-ray analysis of phosphoglycerate kinase 2, a sperm-specific isoform from Mus musculus., Sawyer GM, Monzingo AF, Poteet EC, O'Brien DA, Robertus JD, Proteins. 2007 Nov 14;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18004764 18004764]
 [[Category: Mus musculus]]
-[[Category: Phosphoglycerate kinase]]
+[[Category: Monzingo AF]]
-[[Category: Single protein]]
+[[Category: Poteet EC]]
-[[Category: Monzingo, A F.]]
+[[Category: Robertus JD]]
-[[Category: Poteet, E C.]]
+[[Category: Sawyer GM]]
-[[Category: Robertus, J D.]]
-[[Category: Sawyer, G M.]]
-[[Category: 3PG]]
-[[Category: enzyme-substrate complex]]
-[[Category: phosphoglycerate kinse]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:10:35 2008''