2j3h

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:34, 9 May 2024) (edit) (undo)
 
(8 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2j3h.png|left|200px]]
 
-
<!--
+
==Crystal structure of Arabidopsis thaliana Double Bond Reductase (AT5G16970)-Apo form==
-
The line below this paragraph, containing "STRUCTURE_2j3h", creates the "Structure Box" on the page.
+
<StructureSection load='2j3h' size='340' side='right'caption='[[2j3h]], [[Resolution|resolution]] 2.50&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'>[[2j3h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2J3H 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]] 2.5&#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=2j3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j3h OCA], [https://pdbe.org/2j3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2j3h RCSB], [https://www.ebi.ac.uk/pdbsum/2j3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2j3h ProSAT]</span></td></tr>
-
{{STRUCTURE_2j3h| PDB=2j3h | SCENE= }}
+
</table>
 +
== Function ==
 +
[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]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j3/2j3h_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2j3h ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
===CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA DOUBLE BOND REDUCTASE (AT5G16970)-APO FORM===
+
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<ref>PMID:17028190</ref>
-
 
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
<!--
+
</div>
-
The line below this paragraph, {{ABSTRACT_PUBMED_17028190}}, adds the Publication Abstract to the page
+
<div class="pdbe-citations 2j3h" style="background-color:#fffaf0;"></div>
-
(as it appears on PubMed at http://www.pubmed.gov), where 17028190 is the PubMed ID number.
+
== References ==
-
-->
+
<references/>
-
{{ABSTRACT_PUBMED_17028190}}
+
__TOC__
-
 
+
</StructureSection>
-
==About this Structure==
+
-
2J3H is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J3H OCA].
+
-
 
+
-
==Reference==
+
-
<ref group="xtra">PMID:17028190</ref><references group="xtra"/>
+
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
-
[[Category: Bedgar, D L.]]
+
[[Category: Large Structures]]
-
[[Category: Davin, L B.]]
+
[[Category: Bedgar DL]]
-
[[Category: Harper, A R.]]
+
[[Category: Davin LB]]
-
[[Category: Kang, C.]]
+
[[Category: Harper AR]]
-
[[Category: Kim, S J.]]
+
[[Category: Kang C]]
-
[[Category: Lee, C.]]
+
[[Category: Kim SJ]]
-
[[Category: Lewis, N G.]]
+
[[Category: Lee C]]
-
[[Category: Moinuddin, S G.]]
+
[[Category: Lewis NG]]
-
[[Category: Youn, B.]]
+
[[Category: Moinuddin SG]]
-
[[Category: Apo form]]
+
[[Category: Youn B]]
-
[[Category: Arabidopsis thaliana]]
+
-
[[Category: Nadp]]
+
-
[[Category: Oxidoreductase]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 04:07:20 2009''
+

Current revision

Crystal structure of Arabidopsis thaliana Double Bond Reductase (AT5G16970)-Apo form

PDB ID 2j3h

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2j3h"
Personal tools