This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


5iqy

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "5iqy" [edit=sysop:move=sysop])
Current revision (09:16, 20 March 2024) (edit) (undo)
 
(2 intermediate revisions not shown.)
Line 1: Line 1:
==Structure of apo-Dehydroascorbate Reductase from Pennisetum Glaucum phased by Iodide-SAD method==
==Structure of apo-Dehydroascorbate Reductase from Pennisetum Glaucum phased by Iodide-SAD method==
-
<StructureSection load='5iqy' size='340' side='right' caption='[[5iqy]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+
<StructureSection load='5iqy' size='340' side='right'caption='[[5iqy]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[5iqy]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IQY FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[5iqy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cenchrus_americanus Cenchrus americanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IQY FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</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]] 2.4&#8491;</td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutathione_dehydrogenase_(ascorbate) Glutathione dehydrogenase (ascorbate)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.5.1 1.8.5.1] </span></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></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=5iqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iqy OCA], [http://pdbe.org/5iqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iqy RCSB], [http://www.ebi.ac.uk/pdbsum/5iqy PDBsum]</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=5iqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iqy OCA], [https://pdbe.org/5iqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iqy RCSB], [https://www.ebi.ac.uk/pdbsum/5iqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iqy ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/U5XYA0_CENAM U5XYA0_CENAM]
-
Dehydroascorbate reductase (DHAR), a member of the glutathione-S-transferase (GST) family, reduces dehydroascorbate (DHA) to ascorbate (AsA; Vitamin-C) in a glutathione (GSH)-dependent manner and in doing so, replenishes the critical AsA pool of the cell. To understand the enzyme mechanism in detail, we determined the crystal structure of a plant DHAR from Pennisetum glaucum (PgDHAR) using Iodide-Single Anomalous Dispersion (SAD) and Molecular replacement methods, in two different space groups. Here, we show PgDHAR in complex with two non-native ligands, viz. an acetate bound at the G-site, which resembles the gamma-carboxyl moiety of GSH, and a glycerol at the H-site, which shares the backbone of AsA. We also show that, in the absence of bound native substrates, these non-native ligands help define the critical 'hook points' in the DHAR enzyme active site. Further, our data suggest that these non-native ligands can act as the logical bootstrapping points for iterative design of inhibitors/analogs for DHARs.
+
-
 
+
-
Non-native ligands define the active site of Pennisetum glaucum (L.) R. Br dehydroascorbate reductase.,Krishna Das B, Kumar A, Maindola P, Mahanty S, Jain SK, Reddy MK, Arockiasamy A Biochem Biophys Res Commun. 2016 May 13;473(4):1152-7. doi:, 10.1016/j.bbrc.2016.04.031. Epub 2016 Apr 9. PMID:27067046<ref>PMID:27067046</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 5iqy" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Arockiasamy, A]]
+
[[Category: Cenchrus americanus]]
-
[[Category: Das, B K]]
+
[[Category: Large Structures]]
-
[[Category: Kumar, A]]
+
[[Category: Arockiasamy A]]
-
[[Category: Manidola, P]]
+
[[Category: Das BK]]
-
[[Category: Dehydroascorbate reductase]]
+
[[Category: Kumar A]]
-
[[Category: Iodide-sad method]]
+
[[Category: Manidola P]]
-
[[Category: Oxidoreductase]]
+

Current revision

Structure of apo-Dehydroascorbate Reductase from Pennisetum Glaucum phased by Iodide-SAD method

PDB ID 5iqy

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5iqy"
Personal tools