7qo8: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7qo8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QO8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QO8 FirstGlance]. <br>
<table><tr><td colspan='2'>[[7qo8]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7QO8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7QO8 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.95&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7qo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qo8 OCA], [https://pdbe.org/7qo8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qo8 RCSB], [https://www.ebi.ac.uk/pdbsum/7qo8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qo8 ProSAT]</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=7qo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7qo8 OCA], [https://pdbe.org/7qo8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7qo8 RCSB], [https://www.ebi.ac.uk/pdbsum/7qo8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7qo8 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[https://www.uniprot.org/uniprot/DEGLY_PYRHO DEGLY_PYRHO] Deglycase that catalyzes the deglycation of the Maillard adducts formed between amino groups of proteins and reactive carbonyl groups of glyoxals. Thus, functions as a protein deglycase that repairs methylglyoxal- and glyoxal-glycated proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteine, arginine and lysine residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of advanced glycation endproducts (AGE) that cause irreversible damage (By similarity). Also displays proteolytic activity (PubMed:11114201).[UniProtKB:Q51732]<ref>PMID:11114201</ref>  
[https://www.uniprot.org/uniprot/DEGLY_PYRHO DEGLY_PYRHO] Deglycase that catalyzes the deglycation of the Maillard adducts formed between amino groups of proteins and reactive carbonyl groups of glyoxals. Thus, functions as a protein deglycase that repairs methylglyoxal- and glyoxal-glycated proteins, and releases repaired proteins and lactate or glycolate, respectively. Deglycates cysteine, arginine and lysine residues in proteins, and thus reactivates these proteins by reversing glycation by glyoxals. Acts on early glycation intermediates (hemithioacetals and aminocarbinols), preventing the formation of advanced glycation endproducts (AGE) that cause irreversible damage (By similarity). Also displays proteolytic activity (PubMed:11114201).[UniProtKB:Q51732]<ref>PMID:11114201</ref>  
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Small-angle X-ray scattering (SAXS) has become an indispensable tool in structural biology, complementing atomic-resolution techniques. It is sensitive to the electron-density difference between solubilized biomacromolecules and the buffer, and provides information on molecular masses, particle dimensions and interactions, low-resolution conformations and pair distance-distribution functions. When SAXS data are recorded at multiple contrasts, i.e. at different solvent electron densities, it is possible to probe, in addition to their overall shape, the internal electron-density profile of biomacromolecular assemblies. Unfortunately, contrast-variation SAXS has been limited by the range of solvent electron densities attainable using conventional co-solutes (for example sugars, glycerol and salt) and by the fact that some biological systems are destabilized in their presence. Here, SAXS contrast data from an oligomeric protein and a protein-RNA complex are presented in the presence of iohexol and Gd-HPDO3A, two electron-rich molecules that are used in biomedical imaging and that belong to the families of iodinated and lanthanide-based complexes, respectively. Moderate concentrations of both molecules allowed solvent electron densities matching those of proteins to be attained. While iohexol yielded higher solvent electron densities (per mole), it interacted specifically with the oligomeric protein and precipitated the protein-RNA complex. Gd-HPDO3A, while less efficient (per mole), did not disrupt the structural integrity of either system, and atomic models could be compared with the SAXS data. Due to their elevated solubility and electron density, their chemical inertness, as well as the possibility of altering their physico-chemical properties, lanthanide-based complexes represent a class of molecules with promising potential for contrast-variation SAXS experiments on diverse biomacromolecular systems.
Medical contrast agents as promising tools for biomacromolecular SAXS experiments.,Gabel F, Engilberge S, Schmitt E, Thureau A, Mechulam Y, Perez J, Girard E Acta Crystallogr D Struct Biol. 2022 Sep 1;78(Pt 9):1120-1130. doi: , 10.1107/S2059798322007392. Epub 2022 Aug 9. PMID:36048152<ref>PMID:36048152</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7qo8" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>

Latest revision as of 07:58, 7 February 2024

Structure of Protease1 from Pyrococcus horikoshii in space group 19 with a hexamer in the asymmetric unit

7qo8, resolution 1.95Å

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