4dsr: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:4dsr.png|left|200px]]
-<!--
+==Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in reduced form==
-The line below this paragraph, containing "STRUCTURE_4dsr", creates the "Structure Box" on the page.
+<StructureSection load='4dsr' size='340' side='right'caption='[[4dsr]], [[Resolution|resolution]] 2.91&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[4dsr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DSR FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.91&#8491;</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=4dsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dsr OCA], [https://pdbe.org/4dsr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dsr RCSB], [https://www.ebi.ac.uk/pdbsum/4dsr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dsr ProSAT]</span></td></tr>
-{{STRUCTURE_4dsr|  PDB=4dsr  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AHP1_YEAST AHP1_YEAST] Thiol-specific antioxidant protein with alkyl hydroperoxidase activity. Involved in osmotic stress resistance and detoxification of the cell. Preferentially eliminates organic peroxides rather than H(2)O(2). Involved in cellular Mn(2+) homeostasis.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Peroxiredoxins (Prxs) are thiol-specific antioxidant proteins that protect cells against reactive oxygen species and are involved in cellular signaling pathways. Alkyl hydroperoxide reductase Ahp1 belongs to the Prx5 subfamily and is a two-cysteine (2-Cys) Prx that forms an intermolecular disulfide bond. Enzymatic assays and bioinformatics enabled us to re-assign the peroxidatic cysteine (C(P)) to Cys-62 and the resolving cysteine (C(R)) to Cys-31 but not the previously reported Cys-120. Thus Ahp1 represents the first 2-Cys Prx with a peroxidatic cysteine after the resolving cysteine in the primary sequence. We also found the positive cooperativity of the substrate t-butyl hydroperoxide binding to Ahp1 homodimer at a Hill coefficient of approximately 2, which enabled Ahp1 to eliminate hydroperoxide at much higher efficiency. To gain the structural insights into the catalytic cycle of Ahp1, we determined the crystal structures of Ahp1 in the oxidized, reduced, and Trx2-complexed forms at 2.40, 2.91, and 2.10 A resolution, respectively. Structural superposition of the oxidized to the reduced form revealed significant conformational changes at the segments containing C(P) and C(R). An intermolecular C(P)-C(R) disulfide bond crossing the A-type dimer interface distinguishes Ahp1 from other typical 2-Cys Prxs. The structure of the Ahp1-Trx2 complex showed for the first time how the electron transfers from thioredoxin to a peroxidase with a thioredoxin-like fold. In addition, site-directed mutagenesis in combination with enzymatic assays suggested that the peroxidase activity of Ahp1 would be altered upon the urmylation (covalently conjugated to ubiquitin-related modifier Urm1) of Lys-32.
-===Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in reduced form===
+Structural Snapshots of Yeast Alkyl Hydroperoxide Reductase Ahp1 Peroxiredoxin Reveal a Novel Two-cysteine Mechanism of Electron Transfer to Eliminate Reactive Oxygen Species.,Lian FM, Yu J, Ma XX, Yu XJ, Chen Y, Zhou CZ J Biol Chem. 2012 May 18;287(21):17077-87. Epub 2012 Apr 2. PMID:22474296<ref>PMID:22474296</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4dsr" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_22474296}}, adds the Publication Abstract to the page
+*[[Peroxiredoxin 3D structures|Peroxiredoxin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 22474296 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22474296}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[4dsr]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DSR OCA].
+[[Category: Saccharomyces cerevisiae S288C]]
+[[Category: Chen Y]]
-==Reference==
+[[Category: Lian FM]]
-<ref group="xtra">PMID:022474296</ref><references group="xtra"/>
+[[Category: Ma XX]]
-[[Category: Peroxiredoxin]]
+[[Category: Yu J]]
-[[Category: Saccharomyces cerevisiae]]
+[[Category: Yu XJ]]
-[[Category: Chen, Y.]]
+[[Category: Zhou CZ]]
-[[Category: Lian, F M.]]
-[[Category: Ma, X X.]]
-[[Category: Yu, J.]]
-[[Category: Yu, X J.]]
-[[Category: Zhou, C Z.]]
-[[Category: Alkyl hydroperoxide reductase]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxidase]]
-[[Category: Peroxiredoxin]]
-[[Category: Thioredoxin-like fold]]