5lrd: Difference between revisions

Latest revision as of 18:42, 18 October 2023

Crystal structure of Glycogen Phosphorylase b in complex with KS242

Structural highlights

5lrd is a 1 chain structure with sequence from Oryctolagus cuniculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	DMS, KS2, PLP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

Publication Abstract from PubMed

3-(C-Glucopyranosyl)-5aryl-1,2,4-triazoles with an aryl moiety larger than phenyl have been shown to have strong inhibitory potency (Ki values in the range of upper nM) for human liver glycogen phosphorylase (hlGP), a pharmacologically relevant target for diabetes type 2. In this study we investigate in a comparative manner the inhibitory effect of the above triazoles and their respective imidazoles on hlGPa. Kinetic studies show that the imidazole derivatives are 6-8 times more potent than their corresponding triazoles. We also seek to answer how the type of the aryl moiety affects the potency in hlGPa, and by determination of the crystal structure of rmGPb in complex with the triazole derivatives the structural basis of their inhibitory efficacy is also elucidated. Our studies revealed that the van der Waals interactions between the aryl moiety and residues in a hydrophobic pocket within the active site are mainly responsible for the variations in the potency of these inhibitors.

van der Waals interactions govern C-beta-d-glucopyranosyl triazoles' nM inhibitory potency in human liver glycogen phosphorylase.,Kantsadi AL, Stravodimos GA, Kyriakis E, Chatzileontiadou DSM, Solovou TGA, Kun S, Bokor E, Somsak L, Leonidas DD J Struct Biol. 2017 Jul;199(1):57-67. doi: 10.1016/j.jsb.2017.05.001. Epub 2017, May 5. PMID:28483603^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Kantsadi AL, Stravodimos GA, Kyriakis E, Chatzileontiadou DSM, Solovou TGA, Kun S, Bokor E, Somsak L, Leonidas DD. van der Waals interactions govern C-beta-d-glucopyranosyl triazoles' nM inhibitory potency in human liver glycogen phosphorylase. J Struct Biol. 2017 Jul;199(1):57-67. doi: 10.1016/j.jsb.2017.05.001. Epub 2017, May 5. PMID:28483603 doi:https://dx.doi.org/10.1016/j.jsb.2017.05.001

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Kantsadi AL, Stravodimos GA, Kyriakis E, Chatzileontiadou DSM, Solovou TGA, Kun S, Bokor E, Somsak L, Leonidas DD. van der Waals interactions govern C-beta-d-glucopyranosyl triazoles' nM inhibitory potency in human liver glycogen phosphorylase. J Struct Biol. 2017 Jul;199(1):57-67. doi: 10.1016/j.jsb.2017.05.001. Epub 2017, May 5. PMID:28483603 doi:https://dx.doi.org/10.1016/j.jsb.2017.05.001

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='5lrd' size='340' side='right'caption='[[5lrd]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5lrd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LRD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5LRD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5lrd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LRD FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=KS2:(2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-(4-methylphenyl)-4~{H}-1,2,4-triazol-3-yl]oxane-3,4,5-triol'>KS2</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5lrc|5lrc]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=KS2:(2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-[5-(4-methylphenyl)-4~{H}-1,2,4-triazol-3-yl]oxane-3,4,5-triol'>KS2</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'>[https://proteopedia.org/fgij/fg.htm?mol=5lrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lrd OCA], [https://pdbe.org/5lrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lrd RCSB], [https://www.ebi.ac.uk/pdbsum/5lrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lrd ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5lrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lrd OCA], [http://pdbe.org/5lrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lrd RCSB], [http://www.ebi.ac.uk/pdbsum/5lrd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lrd 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.
+[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.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 29: / Line 28: @@
 [[Category: Large Structures]]
 [[Category: Oryctolagus cuniculus]]
-[[Category: Phosphorylase]]
+[[Category: Kantsadi AL]]
-[[Category: Kantsadi, A L]]
+[[Category: Leonidas DD]]
-[[Category: Leonidas, D D]]
-[[Category: Alpha and beta protein]]
-[[Category: Transferase]]

5lrd: Difference between revisions

Latest revision as of 18:42, 18 October 2023

Crystal structure of Glycogen Phosphorylase b in complex with KS242

Structural highlights

Function

Publication Abstract from PubMed

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References

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