1l5r: Difference between revisions

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-[[Image:1l5r.jpg|left|200px]]<br /><applet load="1l5r" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1l5r, resolution 2.10&Aring;" />
-'''Human liver glycogen phosphorylase a complexed with riboflavin, N-Acetyl-beta-D-Glucopyranosylamine and CP-403,700'''<br />
-==Overview==
+==Human liver glycogen phosphorylase a complexed with riboflavin, N-Acetyl-beta-D-Glucopyranosylamine and CP-403,700==
-Human liver glycogen phosphorylase (HLGP) catalyzes the breakdown of glycogen to maintain serum glucose levels and is a therapeutic target for diabetes. HLGP is regulated by multiple interacting allosteric sites, each of which is a potential drug binding site. We used surface plasmon resonance (SPR) to screen for compounds that bind to the purine allosteric inhibitor site. We determined the affinities of a series of compounds and solved the crystal structures of three representative ligands with K(D) values from 17-550 microM. The crystal structures reveal that the affinities are partly determined by ligand-specific water-mediated hydrogen bonds and side chain movements. These effects could not be predicted; both crystallographic and SPR studies were required to understand the important features of binding and together provide a basis for the design of new allosteric inhibitors targeting this site.
+<StructureSection load='1l5r' size='340' side='right'caption='[[1l5r]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1l5r]] is a 2 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=1L5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L5R 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]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=700:[5-CHLORO-1H-INDOL-2-CARBONYL-PHENYLALANINYL]-AZETIDINE-3-CARBOXYLIC+ACID'>700</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NBG:1-N-ACETYL-BETA-D-GLUCOSAMINE'>NBG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=RBF:RIBOFLAVIN'>RBF</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=1l5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l5r OCA], [https://pdbe.org/1l5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l5r RCSB], [https://www.ebi.ac.uk/pdbsum/1l5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l5r ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN] Defects in PYGL are the cause of glycogen storage disease type 6 (GSD6) [MIM:[https://omim.org/entry/232700 232700]. A metabolic disorder characterized by mild to moderate hypoglycemia, mild ketosis, growth retardation, and prominent hepatomegaly. Heart and skeletal muscle are not affected.<ref>PMID:9529348</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/PYGL_HUMAN PYGL_HUMAN] Phosphorylase is an important allosteric enzyme in carbohydrate metabolism. Enzymes from different sources differ in their regulatory mechanisms and in their natural substrates. However, all known phosphorylases share catalytic and structural properties.
+== 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/l5/1l5r_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=1l5r ConSurf].
+<div style="clear:both"></div>
-==Disease==
+==See Also==
-Known disease associated with this structure: Glycogen storage disease VI OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=232700 232700]]
+*[[Glycogen phosphorylase 3D structures|Glycogen phosphorylase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-L5R 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=NBG:'>NBG</scene>, <scene name='pdbligand=PLP:'>PLP</scene>, <scene name='pdbligand=700:'>700</scene>, <scene name='pdbligand=RBF:'>RBF</scene> and <scene name='pdbligand=MRD:'>MRD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.4.1 2.4.4.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L5R OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Structure-activity analysis of the purine binding site of human liver glycogen phosphorylase., Ekstrom JL, Pauly TA, Carty MD, Soeller WC, Culp J, Danley DE, Hoover DJ, Treadway JL, Gibbs EM, Fletterick RJ, Day YS, Myszka DG, Rath VL, Chem Biol. 2002 Aug;9(8):915-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12204691 12204691]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Transferase]]
+[[Category: Carty MD]]
-[[Category: Carty, M D.]]
+[[Category: Culp J]]
-[[Category: Culp, J.]]
+[[Category: Danley DE]]
-[[Category: Danley, D E.]]
+[[Category: Day YSN]]
-[[Category: Day, Y S.N.]]
+[[Category: Ekstrom JL]]
-[[Category: Ekstrom, J L.]]
+[[Category: Fletterick RJ]]
-[[Category: Fletterick, R J.]]
+[[Category: Gibbs EM]]
-[[Category: Gibbs, E M.]]
+[[Category: Hoover DJ]]
-[[Category: Hoover, D J.]]
+[[Category: Myszka DG]]
-[[Category: Myszka, D G.]]
+[[Category: Pauly TA]]
-[[Category: Pauly, T A.]]
+[[Category: Rath VL]]
-[[Category: Rath, V L.]]
+[[Category: Soeller WC]]
-[[Category: Soeller, W C.]]
+[[Category: Treadway JL]]
-[[Category: Treadway, J L.]]
-[[Category: 700]]
-[[Category: MRD]]
-[[Category: NBG]]
-[[Category: PLP]]
-[[Category: RBF]]
-[[Category: phosphorylase]]
-[[Category: purine site]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:41:38 2008''