2av6
From Proteopedia
(Difference between revisions)
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==X-Ray studies on maltodextrin phosphorylase complexes: recognition of substrates and cathalitic mechanism of phosphorylase family== | ==X-Ray studies on maltodextrin phosphorylase complexes: recognition of substrates and cathalitic mechanism of phosphorylase family== | ||
| - | <StructureSection load='2av6' size='340' side='right'caption='[[2av6]]' scene=''> | + | <StructureSection load='2av6' size='340' side='right'caption='[[2av6]], [[Resolution|resolution]] 2.01Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2AV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AV6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2av6]] 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=2AV6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2AV6 FirstGlance]. <br> |
| - | </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=2av6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2av6 OCA], [https://pdbe.org/2av6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2av6 RCSB], [https://www.ebi.ac.uk/pdbsum/2av6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2av6 ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> |
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1qm5|1qm5]], [[1l5v|1l5v]], [[1l5w|1l5w]], [[1l6i|1l6i]]</div></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">EG10560 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | ||
| + | <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=2av6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2av6 OCA], [https://pdbe.org/2av6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2av6 RCSB], [https://www.ebi.ac.uk/pdbsum/2av6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2av6 ProSAT]</span></td></tr> | ||
</table> | </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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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</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=2av6 ConSurf]. | </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=2av6 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | We report crystal structures of ternary complexes of maltodextrin phosphorylase with natural oligosaccharide and phosphate mimicking anions: nitrate, sulphate and vanadate. Electron density maps obtained from crystals grown in presence of Al(NO3)3 show a nitrate ion instead of the expected AlF4- in the catalytic site. The trigonal NO3- is coplanar with the Arg569 guanidinium group and mimics three of the four oxygen atoms of phosphate. The ternary complex with sulphate shows a partial occupancy of the anionic site. The low affinity of the sulphate ion, observed when the alpha-glucosyl substrate is present in the catalytic channel, is ascribed to restricted space for the anion. Even lower occupancy is observed for the larger vanadate anion. The Malp/G5/VO43- structure shows the partial occupancy of the oligosaccharide and the dislocation of the 380's loop. This has been attributed to the formation of oligosaccharide vanadate derivatives (confirmed by capillary electrophoresis) that reduces their effective concentration. The difficulty to trap a ternary complex mimicking the ground state has been correlated to the apparent lower affinity that natural substrates show regarding the intermediates of the enzymatic reaction. | ||
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| + | X-ray studies on ternary complexes of maltodextrin phosphorylase.,Campagnolo M, Campa C, Zorzi RD, Wuerges J, Geremia S Arch Biochem Biophys. 2008 Mar 1;471(1):11-9. Epub 2007 Dec 28. PMID:18164678<ref>PMID:18164678</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 2av6" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Bacillus coli migula 1895]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Campagnolo M]] | + | [[Category: Phosphorylase]] |
| - | [[Category: Geremia S]] | + | [[Category: Campagnolo, M]] |
| + | [[Category: Geremia, S]] | ||
| + | [[Category: Carbohydrate recognition]] | ||
| + | [[Category: Maltopentaose]] | ||
| + | [[Category: Phosphorylase mechanism]] | ||
| + | [[Category: Ternary complexes with natural and inhibitory substrate]] | ||
| + | [[Category: Transferase]] | ||
Revision as of 06:46, 10 November 2021
X-Ray studies on maltodextrin phosphorylase complexes: recognition of substrates and cathalitic mechanism of phosphorylase family
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