2wu9

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of peroxisomal KAT2 from Arabidopsis thaliana

Structural highlights

2wu9 is a 2 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

THIK2_ARATH Involved in long chain fatty-acid beta-oxidation prior to gluconeogenesis during germination and subsequent seedling growth. Confers sensitivity to 2,4-dichlorophenoxybutiric acid (2,4-DB). Required for local and systemic induction of jasmonic acid (JA) biosynthesis after wounding. Seems to be involved in JA biosynthesis during senescence.^[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

The breakdown of fatty acids, performed by the beta-oxidation cycle, is crucial for plant germination and sustainability. beta-Oxidation involves four enzymatic reactions. The final step, in which a two-carbon unit is cleaved from the fatty acid, is performed by a 3-ketoacyl-CoA thiolase (KAT). The shortened fatty acid may then pass through the cycle again (until reaching acetoacetyl-CoA) or be directed to a different cellular function. Crystal structures of KAT from Arabidopsis thaliana and Helianthus annuus have been solved to 1.5 and 1.8 A resolution, respectively. Their dimeric structures are very similar and exhibit a typical thiolase-like fold; dimer formation and active site conformation appear in an open, active, reduced state. Using an interdisciplinary approach, we confirmed the potential of plant KATs to be regulated by the redox environment in the peroxisome within a physiological range. In addition, co-immunoprecipitation studies suggest an interaction between KAT and the multifunctional protein that is responsible for the preceding two steps in beta-oxidation, which would allow a route for substrate channeling. We suggest a model for this complex based on the bacterial system.

Peroxisomal plant 3-ketoacyl-CoA thiolase structure and activity are regulated by a sensitive redox switch.,Pye VE, Christensen CE, Dyer JH, Arent S, Henriksen A J Biol Chem. 2010 Jul 30;285(31):24078-88. Epub 2010 May 12. PMID:20463027^[6]

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

References

↑ Hayashi M, Toriyama K, Kondo M, Nishimura M. 2,4-Dichlorophenoxybutyric acid-resistant mutants of Arabidopsis have defects in glyoxysomal fatty acid beta-oxidation. Plant Cell. 1998 Feb;10(2):183-95. PMID:9490742
↑ Germain V, Rylott EL, Larson TR, Sherson SM, Bechtold N, Carde JP, Bryce JH, Graham IA, Smith SM. Requirement for 3-ketoacyl-CoA thiolase-2 in peroxisome development, fatty acid beta-oxidation and breakdown of triacylglycerol in lipid bodies of Arabidopsis seedlings. Plant J. 2001 Oct;28(1):1-12. PMID:11696182
↑ He Y, Fukushige H, Hildebrand DF, Gan S. Evidence supporting a role of jasmonic acid in Arabidopsis leaf senescence. Plant Physiol. 2002 Mar;128(3):876-84. PMID:11891244 doi:http://dx.doi.org/10.1104/pp.010843
↑ Cruz Castillo M, Martinez C, Buchala A, Metraux JP, Leon J. Gene-specific involvement of beta-oxidation in wound-activated responses in Arabidopsis. Plant Physiol. 2004 May;135(1):85-94. PMID:15141068 doi:http://dx.doi.org/10.1104/pp.104.039925
↑ Afitlhile MM, Fukushige H, Nishimura M, Hildebrand DF. A defect in glyoxysomal fatty acid beta-oxidation reduces jasmonic acid accumulation in Arabidopsis. Plant Physiol Biochem. 2005 Jun;43(6):603-9. PMID:15979881 doi:http://dx.doi.org/S0981-9428(05)00126-9
↑ Pye VE, Christensen CE, Dyer JH, Arent S, Henriksen A. Peroxisomal plant 3-ketoacyl-CoA thiolase structure and activity are regulated by a sensitive redox switch. J Biol Chem. 2010 Jul 30;285(31):24078-88. Epub 2010 May 12. PMID:20463027 doi:10.1074/jbc.M110.106013

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2wu9"

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF PEROXISOMAL KAT2 FROM ARABIDOPSIS THALIANA==
-<StructureSection load='2wu9' size='340' side='right' caption='[[2wu9]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+==Crystal structure of peroxisomal KAT2 from Arabidopsis thaliana==
+<StructureSection load='2wu9' size='340' side='right'caption='[[2wu9]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2wu9]] is a 2 chain structure with sequence 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=2WU9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WU9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2wu9]] 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=2WU9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WU9 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2c7z|2c7z]], [[2c7y|2c7y]], [[2wua|2wua]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Acetyl-CoA_C-acyltransferase Acetyl-CoA C-acyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.16 2.3.1.16] </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=2wu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wu9 OCA], [https://pdbe.org/2wu9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wu9 RCSB], [https://www.ebi.ac.uk/pdbsum/2wu9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wu9 ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2wu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wu9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2wu9 RCSB], [http://www.ebi.ac.uk/pdbsum/2wu9 PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/THIK2_ARATH THIK2_ARATH] Involved in long chain fatty-acid beta-oxidation prior to gluconeogenesis during germination and subsequent seedling growth. Confers sensitivity to 2,4-dichlorophenoxybutiric acid (2,4-DB). Required for local and systemic induction of jasmonic acid (JA) biosynthesis after wounding. Seems to be involved in JA biosynthesis during senescence.<ref>PMID:9490742</ref> <ref>PMID:11696182</ref> <ref>PMID:11891244</ref> <ref>PMID:15141068</ref> <ref>PMID:15979881</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/wu/2wu9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wu/2wu9_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2wu9 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2wu9" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Thiolase|Thiolase]]
+*[[Thiolase 3D structures|Thiolase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Acetyl-CoA C-acyltransferase]]
 [[Category: Arabidopsis thaliana]]
-[[Category: Arent, S.]]
+[[Category: Large Structures]]
-[[Category: Christensen, C E.]]
+[[Category: Arent S]]
-[[Category: Dyer, J H.]]
+[[Category: Christensen CE]]
-[[Category: Henriksen, A.]]
+[[Category: Dyer JH]]
-[[Category: Pye, V E.]]
+[[Category: Henriksen A]]
-[[Category: Acyltransferase]]
+[[Category: Pye VE]]
-[[Category: Beta oxidation]]
-[[Category: Cysteine oxidation]]
-[[Category: Fatty acid biosynthesis]]
-[[Category: Fatty acid metabolism]]
-[[Category: Lipid metabolism]]
-[[Category: Lipid synthesis]]
-[[Category: Oxylipin biosynthesis]]
-[[Category: Plant lipid metabolism]]
-[[Category: Transferase]]

2wu9

From Proteopedia

Current revision

Crystal structure of peroxisomal KAT2 from Arabidopsis thaliana

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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