6bii: Difference between revisions
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New page: '''Unreleased structure''' The entry 6bii is ON HOLD Authors: Shabalin, I.G., Minor, W. Description: Crystal Structure of Pyrococcus yayanosii Glyoxylate Hydroxypyruvate Reductase in c... |
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==Crystal Structure of Pyrococcus yayanosii Glyoxylate Hydroxypyruvate Reductase in complex with NADP and malonate (re-refinement of 5AOW)== | |||
<StructureSection load='6bii' size='340' side='right'caption='[[6bii]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6bii]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_yayanosii_CH1 Pyrococcus yayanosii CH1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5aow 5aow]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BII OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BII FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></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=6bii FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bii OCA], [https://pdbe.org/6bii PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bii RCSB], [https://www.ebi.ac.uk/pdbsum/6bii PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bii ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/F8AEA4_PYRYC F8AEA4_PYRYC] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Glyoxylate accumulation within cells is highly toxic. In humans, it is associated with hyperoxaluria type 2 (PH2) leading to renal failure. The glyoxylate content within cells is regulated by the NADPH/NADH dependent glyoxylate/hydroxypyruvate reductases (GRHPR). These are highly conserved enzymes with a dual activity as they are able to reduce glyoxylate to glycolate and to convert hydroxypyruvate into D-glycerate. Despite the determination of high-resolution X-ray structures, the substrate recognition mode of this class of enzymes remains unclear. We determined the structure at 2.0 A resolution of a thermostable GRHPR from Archaea as a ternary complex in the presence of D-glycerate and NADPH. This shows a binding mode conserved between human and archeal enzymes. We also determined the first structure of GRHPR in presence of glyoxylate at 1.40 A resolution. This revealed the pivotal role of Leu53 and Trp138 in substrate trafficking. These residues act as gatekeepers at the entrance of a tunnel connecting the active site to protein surface. Taken together, these results allowed us to propose a general model for GRHPR mode of action. | |||
New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases.,Lassalle L, Engilberge S, Madern D, Vauclare P, Franzetti B, Girard E Sci Rep. 2016 Feb 11;6:20629. doi: 10.1038/srep20629. PMID:26865263<ref>PMID:26865263</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6bii" style="background-color:#fffaf0;"></div> | ||
[[Category: Minor | == References == | ||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pyrococcus yayanosii CH1]] | |||
[[Category: Girard E]] | |||
[[Category: Lassalle L]] | |||
[[Category: Minor W]] | |||
[[Category: Shabalin IG]] | |||
Latest revision as of 14:41, 4 October 2023
Crystal Structure of Pyrococcus yayanosii Glyoxylate Hydroxypyruvate Reductase in complex with NADP and malonate (re-refinement of 5AOW)
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