2p9t: Difference between revisions

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-[[Image:2p9t.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2p9t", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2p9t|  PDB=2p9t  |  SCENE=  }}
-'''Crystal Structure of Phosphoglycerate Kinase-2 bound to 3-phosphoglycerate'''
+==Crystal Structure of Phosphoglycerate Kinase-2 bound to 3-phosphoglycerate==
+<StructureSection load='2p9t' size='340' side='right'caption='[[2p9t]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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.
-==Overview==
+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>
-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.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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].
+</div>
+<div class="pdbe-citations 2p9t" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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]
+*[[Phosphoglycerate kinase 3D structures|Phosphoglycerate kinase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[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: Enzyme-substrate complex]]
-[[Category: Phosphoglycerate kinse]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 24 09:26:48 2008''