2ecp: Difference between revisions

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-{{Seed}}
-[[Image:2ecp.png|left|200px]]
-<!--
+==THE CRYSTAL STRUCTURE OF THE E. COLI MALTODEXTRIN PHOSPHORYLASE COMPLEX==
-The line below this paragraph, containing "STRUCTURE_2ecp", creates the "Structure Box" on the page.
+<StructureSection load='2ecp' size='340' side='right'caption='[[2ecp]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2ecp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ECP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ECP FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
--->
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AC1:6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL'>AC1</scene></td></tr>
-{{STRUCTURE_2ecp|  PDB=2ecp  |  SCENE=  }}
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Phosphorylase Phosphorylase], with EC number [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=2ecp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ecp OCA], [https://pdbe.org/2ecp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ecp RCSB], [https://www.ebi.ac.uk/pdbsum/2ecp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ecp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/PHSM_ECOLI PHSM_ECOLI]] 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/ec/2ecp_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=2ecp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Acarbose is a naturally occurring pseudo-tetrasaccharide. It has been used in conjunction with other drugs in the treatment of diabetes where it acts as an inhibitor of intestinal glucosidases. To probe the interactions of acarbose with other carbohydrate recognition enzymes, the crystal structure of E. coli maltodextrin phosphorylase (MalP) complexed with acarbose has been determined at 2.95 A resolution and refined to crystallographic R-values of R (Rfree) = 0.241 (0.293), respectively. Acarbose adopts a conformation that is close to its major minimum free energy conformation in the MalP-acarbose structure. The acarviosine moiety of acarbose occupies sub-sites +1 and +2 and the disaccharide sub-sites +3 and +4. (The site of phosphorolysis is between sub-sites -1 and +1.) This is the first identification of sub-sites +3 and +4 of MalP. Interactions of the glucosyl residues in sub-sites +2 and +4 are dominated by carbohydrate stacking interactions with tyrosine residues. These tyrosines (Tyr280 and Tyr613, respectively, in the rabbit muscle phosphorylase numbering scheme) are conserved in all species of phosphorylase. A glycerol molecule from the cryoprotectant occupies sub-site -1. The identification of four oligosaccharide sub-sites, that extend from the interior of the phosphorylase close to the catalytic site to the exterior surface of MalP, provides a structural rationalization of the substrate selectivity of MalP for a pentasaccharide substrate. Crystallographic binding studies of acarbose with amylases, glucoamylases, and glycosyltranferases and NMR studies of acarbose in solution have shown that acarbose can adopt two different conformations. This flexibility allows acarbose to target a number of different enzymes. The two alternative conformations of acarbose when bound to different carbohydrate enzymes are discussed.
-===THE CRYSTAL STRUCTURE OF THE E. COLI MALTODEXTRIN PHOSPHORYLASE COMPLEX===
+The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex.,O'Reilly M, Watson KA, Johnson LN Biochemistry. 1999 Apr 27;38(17):5337-45. PMID:10220320<ref>PMID:10220320</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_10220320}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2ecp" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 10220320 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10220320}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bacillus coli migula 1895]]
-ECP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ECP OCA].
+[[Category: Large Structures]]
-==Reference==
-The crystal structure of the Escherichia coli maltodextrin phosphorylase-acarbose complex., O'Reilly M, Watson KA, Johnson LN, Biochemistry. 1999 Apr 27;38(17):5337-45. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10220320 10220320]
-[[Category: Escherichia coli]]
 [[Category: Phosphorylase]]
-[[Category: Single protein]]
+[[Category: Johnson, L N]]
-[[Category: Johnson, L N.]]
+[[Category: Reilly, M O]]
-[[Category: Reilly, M O.]]
+[[Category: Watson, K A]]
-[[Category: Watson, K A.]]
 [[Category: Acarbose]]
 [[Category: Diabetes]]
 [[Category: Glycosyltransferase]]
 [[Category: Malp]]
-[[Category: Phosphorylase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 18:23:03 2008''