6k40: Difference between revisions

Latest revision as of 10:26, 22 November 2023

Crystal structure of alkyl hydroperoxide reductase from D. radiodurans R1

Structural highlights

6k40 is a 12 chain structure with sequence from Deinococcus radiodurans R1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.27Å
Ligands:	GOL, PEG, TRS
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9RTJ7_DEIRA

Publication Abstract from PubMed

Deinococcus radiodurans is well known for its extreme resistance to ionizing radiation (IR). Since reactive oxygen species generated by IR can damage various cellular components, D. radiodurans has developed effective antioxidant systems to cope with this oxidative stress. dr1765 from D. radiodurans is predicted to encode an alkyl hydroperoxidase-like protein (AhpD family), which is implicated in the reduction of hydrogen peroxide (H2O2) and organic hydroperoxides. In this study, we constructed a dr1765 mutant strain (Deltadr1765) and examined the survival rate after H2O2 treatment. Deltadr1765 showed a significant decrease in the H2O2 resistance compared to the wild-type strain. We also determined the crystal structure of DR1765 at 2.27 A resolution. DR1765 adopted an all alpha helix protein fold representative of the AhpD-like superfamily. Structural comparisons of DR1765 with its structural homologues revealed that DR1765 possesses the Glu74-Cys86-Tyr88-Cys89-His93 signature motif, which is conserved in the proton relay system of AhpD. Complementation of Deltadr1765 with dr1765 encoding C86A or C89A mutation failed to restore the survival rate to wild-type level. Taken together, these results suggest that DR1765 might function as an AhpD to protect cells from oxidative stress.

Crystal structure of the AhpD-like protein DR1765 from Deinococcus radiodurans R1.,Zhao L, Jeong S, Zhang J, Jung JH, Choi JI, Lim S, Kim MK Biochem Biophys Res Commun. 2020 Aug 20;529(2):444-449. doi:, 10.1016/j.bbrc.2020.06.061. Epub 2020 Jul 1. PMID:32703449^[1]

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

References

↑ Zhao L, Jeong S, Zhang J, Jung JH, Choi JI, Lim S, Kim MK. Crystal structure of the AhpD-like protein DR1765 from Deinococcus radiodurans R1. Biochem Biophys Res Commun. 2020 Aug 20;529(2):444-449. doi:, 10.1016/j.bbrc.2020.06.061. Epub 2020 Jul 1. PMID:32703449 doi:https://dx.doi.org/10.1016/j.bbrc.2020.06.061

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OCA

[1] Zhao L, Jeong S, Zhang J, Jung JH, Choi JI, Lim S, Kim MK. Crystal structure of the AhpD-like protein DR1765 from Deinococcus radiodurans R1. Biochem Biophys Res Commun. 2020 Aug 20;529(2):444-449. doi:, 10.1016/j.bbrc.2020.06.061. Epub 2020 Jul 1. PMID:32703449 doi:https://dx.doi.org/10.1016/j.bbrc.2020.06.061

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6k40' size='340' side='right'caption='[[6k40]], [[Resolution|resolution]] 2.27&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6k40]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K40 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6K40 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6k40]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K40 FirstGlance]. <br>
-</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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.27&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DR_1765 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6k40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k40 OCA], [https://pdbe.org/6k40 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k40 RCSB], [https://www.ebi.ac.uk/pdbsum/6k40 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k40 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6k40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k40 OCA], [http://pdbe.org/6k40 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k40 RCSB], [http://www.ebi.ac.uk/pdbsum/6k40 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k40 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9RTJ7_DEIRA Q9RTJ7_DEIRA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Deira]]
+[[Category: Deinococcus radiodurans R1]]
 [[Category: Large Structures]]
-[[Category: Peroxiredoxin]]
+[[Category: Kim M-K]]
-[[Category: Kim, M K]]
+[[Category: Zhang J]]
-[[Category: Zhang, J]]
+[[Category: Zhao L]]
-[[Category: Zhao, L]]
-[[Category: Antioxidant]]
-[[Category: Hydrogen peroxide]]
-[[Category: Oxidoreductase]]
-[[Category: Stress resistance]]

6k40: Difference between revisions

Latest revision as of 10:26, 22 November 2023

Crystal structure of alkyl hydroperoxide reductase from D. radiodurans R1

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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