4dss

From Proteopedia

(Difference between revisions)

Revision as of 08:36, 21 September 2022

Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in complex with thioredoxin Trx2

Structural highlights

4dss is a 2 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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.

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.

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^[1]

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

References

↑ Lian FM, Yu J, Ma XX, Yu XJ, Chen Y, Zhou CZ. Structural Snapshots of Yeast Alkyl Hydroperoxide Reductase Ahp1 Peroxiredoxin Reveal a Novel Two-cysteine Mechanism of Electron Transfer to Eliminate Reactive Oxygen Species. J Biol Chem. 2012 May 18;287(21):17077-87. Epub 2012 Apr 2. PMID:22474296 doi:10.1074/jbc.M112.357368

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4dss"

@@ Line 1: / Line 1: @@
 ==Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in complex with thioredoxin Trx2==
-<StructureSection load='4dss' size='340' side='right' caption='[[4dss]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='4dss' size='340' side='right'caption='[[4dss]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4dss]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DSS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DSS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4dss]] is a 2 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=4DSS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4DSS FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4dsq|4dsq]], [[4dsr|4dsr]]</td></tr>
+</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=4dss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dss OCA], [https://pdbe.org/4dss PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4dss RCSB], [https://www.ebi.ac.uk/pdbsum/4dss PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4dss ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AHP1, L2916, L9354.5, YLR109W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), G7746, TRX1, TRX2, YGR209C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></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=4dss FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dss OCA], [http://pdbe.org/4dss PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4dss RCSB], [http://www.ebi.ac.uk/pdbsum/4dss PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4dss ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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. [[http://www.uniprot.org/uniprot/TRX2_YEAST TRX2_YEAST]] Participates as a hydrogen donor in redox reactions through the reversible oxidation of its active center dithiol to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. It is involved in many cellular processes, including deoxyribonucleotide synthesis, repair of oxidatively damaged proteins, protein folding, sulfur metabolism, and redox homeostasis. Thioredoxin-dependent enzymes include phosphoadenosine-phosphosulfate reductase MET16, alkyl-hydroperoxide reductase DOT5, thioredoxin peroxidases TSA1 and TSA2, alkyl hydroperoxide reductase AHP1, and peroxiredoxin HYR1. Thioredoxin is also involved in protection against reducing stress. As part of the LMA1 complex, it is involved in the facilitation of vesicle fusion such as homotypic vacuole and ER-derived COPII vesicle fusion with the Golgi. This activity does not require the redox mechanism. Through its capacity to inactivate the stress response transcription factor YAP1 and its regulator the hydroperoxide stress sensor HYR1, it is involved in feedback regulation of stress response gene expression upon oxidative stress.<ref>PMID:3060034</ref> <ref>PMID:9015301</ref> <ref>PMID:9657146</ref> <ref>PMID:10681558</ref> <ref>PMID:9988687</ref> <ref>PMID:11013218</ref> <ref>PMID:12437921</ref> <ref>PMID:12410842</ref> <ref>PMID:11169096</ref> <ref>PMID:12914955</ref>
+[[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 ==
@@ Line 22: / Line 19: @@
 ==See Also==
-*[[Peroxiredoxin|Peroxiredoxin]]
+*[[Peroxiredoxin 3D structures|Peroxiredoxin 3D structures]]
-*[[Thioredoxin|Thioredoxin]]
+*[[Thioredoxin 3D structures|Thioredoxin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
+[[Category: Large Structures]]
-[[Category: Peroxiredoxin]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Chen, Y]]
+[[Category: Chen Y]]
-[[Category: Lian, F M]]
+[[Category: Lian FM]]
-[[Category: Ma, X X]]
+[[Category: Ma XX]]
-[[Category: Yu, J]]
+[[Category: Yu J]]
-[[Category: Yu, X J]]
+[[Category: Yu XJ]]
-[[Category: Zhou, C Z]]
+[[Category: Zhou CZ]]
-[[Category: Alkyl hydroperoxide reductase]]
-[[Category: Electron transport]]
-[[Category: Oxidoreductase]]
-[[Category: Oxidoreductase-transport protein complex]]
-[[Category: Thioredoxin fold]]
-[[Category: Thioredoxin-2]]
-[[Category: Thioredoxin-like fold]]

4dss

From Proteopedia

Revision as of 08:36, 21 September 2022

Crystal structure of peroxiredoxin Ahp1 from Saccharomyces cerevisiae in complex with thioredoxin Trx2

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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