2j3j

From Proteopedia

(Difference between revisions)

Revision as of 11:24, 31 March 2021

Crystal structure of Arabidopsis thaliana Double Bond Reductase (AT5G16970)-Ternary Complex I

Structural highlights

2j3j is a 2 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	2j3h, 2j3i, 2j3k
Gene:	AER, P1, At5g16970, F2K13_120 (ARATH)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[AER_ARATH] Involved in the detoxification of reactive carbonyls (PubMed:10848984, PubMed:12514241, PubMed:16299173). Acts on lipid peroxide-derived reactive aldehydes (PubMed:12514241). Specific to a double bond activated by an adjacent carbonyl group (PubMed:12514241). Can use both quinones and diamide as substrates, but not menadione, ferricyanide or phylloquinone (PubMed:10848984). Can use 4-hydroxy-(2E)-nonenal (HNE), 4-hydroxy-(2E)-hexenal (HHE), (2E)-nonenal, (2E)-hexenal, (2E)-pentenal, propenal (acrolein), 3-buten-2-one and 3-penten-2-one, but not (R)-(-)-carvone, n-nonanal, n-hexanal, (3Z)-hexanal, cyclohex-2-en-1-one or 12-oxo phytodienoic acid (OPDA) as electron acceptors (PubMed:12514241). Catalyzes the reduction of the alpha,beta-unsaturated bond of 2-alkenals, of lipid peroxide-derived oxenes 9-oxo-10(E),12(Z)-octadecadienoic acid (9-KODE) and 13-oxo-9(Z),11(E)-octadecadienoic acid (13-KODE), as well as 4-oxo-(2E)-nonenal and 4-hydroxynonenal (PubMed:16299173). Can use 12-oxo-10(E) dodecanoate (traumatin), trans-1,3 diphenyl-2-propenone, trans-1,4-diphenyl-2-butene-1,4-dione, 9-oxo-12,13-epoxy-(10E)-octadecenoic acid (trans-EKODE-1b) and 9,13-dihydroxy-10-oxo-11-octadecenoic acid as substrates (PubMed:26678323). Catalyzes the reduction of the 7-8 double bond of phenylpropanal substrates, such as p-coumaryl aldehyde and coniferyl aldehyde (in vitro) (PubMed:17028190). Has activity towards toxic substrates, such as 4-hydroxy-(2E)-nonenal (in vitro) (PubMed:17028190). May play a distinct role in plant antioxidant defense and is possibly involved in NAD(P)/NAD(P)H homeostasis (PubMed:17028190).^[1] ^[2] ^[3] ^[4] ^[5]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

In this study, we determined the crystal structures of the apoform, binary, and ternary complexes of the Arabidopsis alkenal double bond reductase encoded by At5g16970. This protein, one of 11 homologues in Arabidopsis thaliana, is most closely related to the Pinus taeda phenylpropenal double bond reductase, involved in, for example, heartwood formation. Both enzymes also have essential roles in plant defense, and can function by catalyzing the reduction of the 7-8-double bond of phenylpropanal substrates, such as p-coumaryl and coniferyl aldehydes in vitro. At5g16970 is also capable of reducing toxic substrates with the same alkenal functionality, such as 4-hydroxy-(2E)-nonenal. The overall fold of At5g16970 is similar to that of the zinc-independent medium chain dehydrogenase/reductase superfamily, the members of which have two domains and are dimeric in nature, i.e. in contrast to their original classification as being zinc-containing oxidoreductases. As provisionally anticipated from the kinetic data, the shape of the binding pocket can readily accommodate p-coumaryl aldehyde, coniferyl aldehyde, 4-hydroxy-(2E)-nonenal, and 2-alkenals. However, the enzyme kinetic data among these potential substrates differ, favoring p-coumaryl aldehyde. Tyr-260 is provisionally proposed to function as a general acid/base for hydride transfer. A catalytic mechanism for this reduction, and its applicability to related important detoxification mammalian proteins, is also proposed.

Mechanistic and structural studies of apoform, binary, and ternary complexes of the Arabidopsis alkenal double bond reductase At5g16970.,Youn B, Kim SJ, Moinuddin SG, Lee C, Bedgar DL, Harper AR, Davin LB, Lewis NG, Kang C J Biol Chem. 2006 Dec 29;281(52):40076-88. Epub 2006 Oct 6. PMID:17028190^[6]

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

References

↑ Mano J, Babiychuk E, Belles-Boix E, Hiratake J, Kimura A, Inze D, Kushnir S, Asada K. A novel NADPH:diamide oxidoreductase activity in arabidopsis thaliana P1 zeta-crystallin. Eur J Biochem. 2000 Jun;267(12):3661-71. PMID:10848984
↑ Mano J, Torii Y, Hayashi S, Takimoto K, Matsui K, Nakamura K, Inze D, Babiychuk E, Kushnir S, Asada K. The NADPH:quinone oxidoreductase P1-zeta-crystallin in Arabidopsis catalyzes the alpha,beta-hydrogenation of 2-alkenals: detoxication of the lipid peroxide-derived reactive aldehydes. Plant Cell Physiol. 2002 Dec;43(12):1445-55. PMID:12514241
↑ Mano J, Belles-Boix E, Babiychuk E, Inze D, Torii Y, Hiraoka E, Takimoto K, Slooten L, Asada K, Kushnir S. Protection against photooxidative injury of tobacco leaves by 2-alkenal reductase. Detoxication of lipid peroxide-derived reactive carbonyls. Plant Physiol. 2005 Dec;139(4):1773-83. doi: 10.1104/pp.105.070391. Epub 2005 Nov, 18. PMID:16299173 doi:http://dx.doi.org/10.1104/pp.105.070391
↑ Youn B, Kim SJ, Moinuddin SG, Lee C, Bedgar DL, Harper AR, Davin LB, Lewis NG, Kang C. Mechanistic and structural studies of apoform, binary, and ternary complexes of the Arabidopsis alkenal double bond reductase At5g16970. J Biol Chem. 2006 Dec 29;281(52):40076-88. Epub 2006 Oct 6. PMID:17028190 doi:http://dx.doi.org/10.1074/jbc.M605900200
↑ Curien G, Giustini C, Montillet JL, Mas-Y-Mas S, Cobessi D, Ferrer JL, Matringe M, Grechkin A, Rolland N. The chloroplast membrane associated ceQORH putative quinone oxidoreductase reduces long-chain, stress-related oxidized lipids. Phytochemistry. 2016 Feb;122:45-55. doi: 10.1016/j.phytochem.2015.11.015. Epub, 2015 Dec 8. PMID:26678323 doi:http://dx.doi.org/10.1016/j.phytochem.2015.11.015
↑ Youn B, Kim SJ, Moinuddin SG, Lee C, Bedgar DL, Harper AR, Davin LB, Lewis NG, Kang C. Mechanistic and structural studies of apoform, binary, and ternary complexes of the Arabidopsis alkenal double bond reductase At5g16970. J Biol Chem. 2006 Dec 29;281(52):40076-88. Epub 2006 Oct 6. PMID:17028190 doi:http://dx.doi.org/10.1074/jbc.M605900200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2j3j"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Arabidopsis thaliana Double Bond Reductase (AT5G16970)-Ternary Complex I==
-<StructureSection load='2j3j' size='340' side='right' caption='[[2j3j]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='2j3j' size='340' side='right'caption='[[2j3j]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2j3j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2J3J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2j3j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J3J FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2j3h|2j3h]], [[2j3i|2j3i]], [[2j3k|2j3k]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2j3h|2j3h]], [[2j3i|2j3i]], [[2j3k|2j3k]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AER, P1, At5g16970, F2K13_120 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AER, P1, At5g16970, F2K13_120 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=2j3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j3j OCA], [http://pdbe.org/2j3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j3j RCSB], [http://www.ebi.ac.uk/pdbsum/2j3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2j3j 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=2j3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j3j OCA], [https://pdbe.org/2j3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j3j RCSB], [https://www.ebi.ac.uk/pdbsum/2j3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j3j ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/AER_ARATH AER_ARATH]] Involved in the detoxification of reactive carbonyls (PubMed:10848984, PubMed:12514241, PubMed:16299173). Acts on lipid peroxide-derived reactive aldehydes (PubMed:12514241). Specific to a double bond activated by an adjacent carbonyl group (PubMed:12514241). Can use both quinones and diamide as substrates, but not menadione, ferricyanide or phylloquinone (PubMed:10848984). Can use 4-hydroxy-(2E)-nonenal (HNE), 4-hydroxy-(2E)-hexenal (HHE), (2E)-nonenal, (2E)-hexenal, (2E)-pentenal, propenal (acrolein), 3-buten-2-one and 3-penten-2-one, but not (R)-(-)-carvone, n-nonanal, n-hexanal, (3Z)-hexanal, cyclohex-2-en-1-one or 12-oxo phytodienoic acid (OPDA) as electron acceptors (PubMed:12514241). Catalyzes the reduction of the alpha,beta-unsaturated bond of 2-alkenals, of lipid peroxide-derived oxenes 9-oxo-10(E),12(Z)-octadecadienoic acid (9-KODE) and 13-oxo-9(Z),11(E)-octadecadienoic acid (13-KODE), as well as 4-oxo-(2E)-nonenal and 4-hydroxynonenal (PubMed:16299173). Can use 12-oxo-10(E) dodecanoate (traumatin), trans-1,3 diphenyl-2-propenone, trans-1,4-diphenyl-2-butene-1,4-dione, 9-oxo-12,13-epoxy-(10E)-octadecenoic acid (trans-EKODE-1b) and 9,13-dihydroxy-10-oxo-11-octadecenoic acid as substrates (PubMed:26678323). Catalyzes the reduction of the 7-8 double bond of phenylpropanal substrates, such as p-coumaryl aldehyde and coniferyl aldehyde (in vitro) (PubMed:17028190). Has activity towards toxic substrates, such as 4-hydroxy-(2E)-nonenal (in vitro) (PubMed:17028190). May play a distinct role in plant antioxidant defense and is possibly involved in NAD(P)/NAD(P)H homeostasis (PubMed:17028190).<ref>PMID:10848984</ref> <ref>PMID:12514241</ref> <ref>PMID:16299173</ref> <ref>PMID:17028190</ref> <ref>PMID:26678323</ref>
+[[https://www.uniprot.org/uniprot/AER_ARATH AER_ARATH]] Involved in the detoxification of reactive carbonyls (PubMed:10848984, PubMed:12514241, PubMed:16299173). Acts on lipid peroxide-derived reactive aldehydes (PubMed:12514241). Specific to a double bond activated by an adjacent carbonyl group (PubMed:12514241). Can use both quinones and diamide as substrates, but not menadione, ferricyanide or phylloquinone (PubMed:10848984). Can use 4-hydroxy-(2E)-nonenal (HNE), 4-hydroxy-(2E)-hexenal (HHE), (2E)-nonenal, (2E)-hexenal, (2E)-pentenal, propenal (acrolein), 3-buten-2-one and 3-penten-2-one, but not (R)-(-)-carvone, n-nonanal, n-hexanal, (3Z)-hexanal, cyclohex-2-en-1-one or 12-oxo phytodienoic acid (OPDA) as electron acceptors (PubMed:12514241). Catalyzes the reduction of the alpha,beta-unsaturated bond of 2-alkenals, of lipid peroxide-derived oxenes 9-oxo-10(E),12(Z)-octadecadienoic acid (9-KODE) and 13-oxo-9(Z),11(E)-octadecadienoic acid (13-KODE), as well as 4-oxo-(2E)-nonenal and 4-hydroxynonenal (PubMed:16299173). Can use 12-oxo-10(E) dodecanoate (traumatin), trans-1,3 diphenyl-2-propenone, trans-1,4-diphenyl-2-butene-1,4-dione, 9-oxo-12,13-epoxy-(10E)-octadecenoic acid (trans-EKODE-1b) and 9,13-dihydroxy-10-oxo-11-octadecenoic acid as substrates (PubMed:26678323). Catalyzes the reduction of the 7-8 double bond of phenylpropanal substrates, such as p-coumaryl aldehyde and coniferyl aldehyde (in vitro) (PubMed:17028190). Has activity towards toxic substrates, such as 4-hydroxy-(2E)-nonenal (in vitro) (PubMed:17028190). May play a distinct role in plant antioxidant defense and is possibly involved in NAD(P)/NAD(P)H homeostasis (PubMed:17028190).<ref>PMID:10848984</ref> <ref>PMID:12514241</ref> <ref>PMID:16299173</ref> <ref>PMID:17028190</ref> <ref>PMID:26678323</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 35: @@
 </StructureSection>
 [[Category: Arath]]
+[[Category: Large Structures]]
 [[Category: Bedgar, D L]]
 [[Category: Davin, L B]]

2j3j

From Proteopedia

Revision as of 11:24, 31 March 2021

Crystal structure of Arabidopsis thaliana Double Bond Reductase (AT5G16970)-Ternary Complex I

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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