1kti: Difference between revisions

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-[[Image:1kti.gif|left|200px]]<br /><applet load="1kti" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1kti, resolution 1.97&Aring;" />
-'''BINDING OF 100 MM N-ACETYL-N'-BETA-D-GLUCOPYRANOSYL UREA TO GLYCOGEN PHOSPHORYLASE B: KINETIC AND CRYSTALLOGRAPHIC STUDIES'''<br />
-==Overview==
+==BINDING OF 100 MM N-ACETYL-N'-BETA-D-GLUCOPYRANOSYL UREA TO GLYCOGEN PHOSPHORYLASE B: KINETIC AND CRYSTALLOGRAPHIC STUDIES==
-Two substituted ureas of beta-D-glucose, N-acetyl-N'-beta-D-glucopyranosyl urea (Acurea) and N-benzoyl-N'-beta-D-glucopyranosyl urea (Bzurea), have been identified as inhibitors of glycogen phosphorylase, a potential target for therapeutic intervention in type 2 diabetes. To elucidate the structural basis of inhibition, we determined the structure of muscle glycogen phosphorylase b (GPb) complexed with the two compounds at 2.0 A and 1.8 A resolution, respectively. The structure of the GPb-Acurea complex reveals that the inhibitor can be accommodated in the catalytic site of T-state GPb with very little change in the tertiary structure. The glucopyranose moiety makes the standard hydrogen bonds and van der Waals contacts as observed in the GPb-glucose complex, while the acetyl urea moiety is in a favourable electrostatic environment and makes additional polar contacts with the protein. The structure of the GPb-Bzurea complex shows that Bzurea binds tightly at the catalytic site and induces substantial conformational changes in the vicinity of the catalytic site. In particular, the loop of the polypeptide chain containing residues 282-287 shifts 1.3-3.7 A (Calpha atoms) to accommodate Bzurea. Bzurea can also occupy the new allosteric site, some 33 A from the catalytic site, which is currently the target for the design of antidiabetic drugs.
+<StructureSection load='1kti' size='340' side='right'caption='[[1kti]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1kti]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1k0q 1k0q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KTI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KTI 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]] 1.97&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZC:N-ACETYL-N-BETA-D-GLUCOPYRANOSYL+UREA'>AZC</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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=1kti FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kti OCA], [https://pdbe.org/1kti PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kti RCSB], [https://www.ebi.ac.uk/pdbsum/1kti PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kti ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PYGM_RABIT PYGM_RABIT] 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/kt/1kti_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=1kti ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-KTI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with <scene name='pdbligand=AZC:'>AZC</scene> and <scene name='pdbligand=PLP:'>PLP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1K0Q. Active as [http://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.1 2.4.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KTI OCA].
+*[[Glycogen phosphorylase 3D structures|Glycogen phosphorylase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies., Oikonomakos NG, Kosmopoulou M, Zographos SE, Leonidas DD, Chrysina ED, Somsak L, Nagy V, Praly JP, Docsa T, Toth B, Gergely P, Eur J Biochem. 2002 Mar;269(6):1684-96. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11895439 11895439]
+[[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
-[[Category: Phosphorylase]]
+[[Category: Chrysina ED]]
-[[Category: Single protein]]
+[[Category: Docsa T]]
-[[Category: Chrysina, E D.]]
+[[Category: Gergely P]]
-[[Category: Docsa, T.]]
+[[Category: Kosmopoulou M]]
-[[Category: Gergely, P.]]
+[[Category: Leonidas DD]]
-[[Category: Kosmopoulou, M.]]
+[[Category: Nagy V]]
-[[Category: Leonidas, D D.]]
+[[Category: Oikonomakos NG]]
-[[Category: Nagy, V.]]
+[[Category: Praly JP]]
-[[Category: Oikonomakos, N G.]]
+[[Category: Somsak L]]
-[[Category: Praly, J P.]]
+[[Category: Toth B]]
-[[Category: Somsak, L.]]
+[[Category: Zographos SE]]
-[[Category: Toth, B.]]
-[[Category: Zographos, S E.]]
-[[Category: AZC]]
-[[Category: PLP]]
-[[Category: glycogenolysis]]
-[[Category: type 2 diabetes]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:37:45 2008''