8gpb: Difference between revisions

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-[[Image:8gpb.png|left|200px]]
-{{STRUCTURE_8gpb|  PDB=8gpb  |  SCENE=  }}
+==STRUCTURAL MECHANISM FOR GLYCOGEN PHOSPHORYLASE CONTROL BY PHOSPHORYLATION AND AMP==
+<StructureSection load='8gpb' size='340' side='right' caption='[[8gpb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8gpb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/European_rabbit European rabbit]. The December 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Glycogen Phosphorylase''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_12 10.2210/rcsb_pdb/mom_2001_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8GPB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8GPB FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=8gpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8gpb OCA], [http://pdbe.org/8gpb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=8gpb RCSB], [http://www.ebi.ac.uk/pdbsum/8gpb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=8gpb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://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/gp/8gpb_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=8gpb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of activated R state glycogen phosphorylase a (GPa) and R and T state glycogen phosphorylase b (GPb) complexed with AMP have been solved at 2.9 A, 2.9 A and 2.2 A resolution, respectively. The structure of R state GPa is nearly identical to the structure of sulphate-activated R state GPb, except in the region of Ser14, where there is a covalently attached phosphate group in GPa and a non-covalently attached sulphate group in GPb. The contacts made by the N-terminal tail residues in R state GPa at the subunit interface of the functionally active dimer are similar to those observed previously for T state GPa. The quaternary and tertiary structural changes on the T to R transition allow these interactions to be relayed to the catalytic site in R state GPa. The transition from the T state GPb structure to the R state GPa structure results in a change in the N-terminal residues from a poorly ordered extended structure that makes intrasubunit contacts to an ordered coiled conformation that makes intersubunit contacts. The distance between Arg10, the first residue to be located from the N terminus, in R state GPa and T state GPb is 50 A. One of the important subunit-subunit interactions in the dimer molecule involves contacts between the helix alpha 2 and the cap' (residues 35' to 45' that form a loop between the 1st and 2nd alpha helices, alpha 1' and alpha 2' of the other subunit. The prime denotes residues from the other subunit). The interactions made by the N-terminal residues induce structural changes at the cap'/alpha 2 helix interface that lead to the creation of a high-affinity AMP site. The tertiary structural changes at the cap (shifts 1.2 to 2.1 A for residues 35 to 45) are partially compensated by the quaternary structural change so that the overall shifts in these residues after the combined tertiary and quaternary changes are between 0.5 and 1.3 A. AMP binds to R state GPb with at least 100-fold greater affinity and exhibits four additional hydrogen bonds, stronger ionic interactions and more extensive van der Waals' interactions with 116 A2 greater solvent accessible surface area buried compared with AMP bound to T state GPb.(ABSTRACT TRUNCATED AT 400 WORDS)
-===STRUCTURAL MECHANISM FOR GLYCOGEN PHOSPHORYLASE CONTROL BY PHOSPHORYLATION AND AMP===
+Structural mechanism for glycogen phosphorylase control by phosphorylation and AMP.,Barford D, Hu SH, Johnson LN J Mol Biol. 1991 Mar 5;218(1):233-60. PMID:1900534<ref>PMID:1900534</ref>
-{{ABSTRACT_PUBMED_1900534}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 8gpb" style="background-color:#fffaf0;"></div>
-[[8gpb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. The December 2001 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Glycogen Phosphorylase''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2001_12 10.2210/rcsb_pdb/mom_2001_12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8GPB OCA].
+== References ==
+<references/>
-==See Also==
+__TOC__
-*[[Glycogen Phosphorylase|Glycogen Phosphorylase]]
+</StructureSection>
+[[Category: European rabbit]]
-==Reference==
-<ref group="xtra">PMID:001900534</ref><references group="xtra"/>
 [[Category: Glycogen Phosphorylase]]
-[[Category: Oryctolagus cuniculus]]
 [[Category: Phosphorylase]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Barford, D.]]
+[[Category: Barford, D]]
-[[Category: Hu, S H.]]
+[[Category: Hu, S H]]
-[[Category: Johnson, L N.]]
+[[Category: Johnson, L N]]
 [[Category: Glycogen phosphorylase]]