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| | ==Crystal structure of GH3.12 from Arabidopsis thaliana in complex with AMPCPP and salicylate== | | ==Crystal structure of GH3.12 from Arabidopsis thaliana in complex with AMPCPP and salicylate== |
| - | <StructureSection load='4l39' size='340' side='right' caption='[[4l39]], [[Resolution|resolution]] 2.81Å' scene=''> | + | <StructureSection load='4l39' size='340' side='right'caption='[[4l39]], [[Resolution|resolution]] 2.81Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4l39]] 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=4L39 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L39 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4l39]] 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=4L39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L39 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APC:DIPHOSPHOMETHYLPHOSPHONIC+ACID+ADENOSYL+ESTER'>APC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SAL:2-HYDROXYBENZOIC+ACID'>SAL</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4epm|4epm]], [[4ewv|4ewv]], [[4eq4|4eq4]], [[4eql|4eql]]</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=4l39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l39 OCA], [https://pdbe.org/4l39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l39 RCSB], [https://www.ebi.ac.uk/pdbsum/4l39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l39 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GH3.12, GDG1, PBS3, WIN3, At5g13320, T22N19.5, T31B5.140 ([http://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=4l39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l39 OCA], [http://pdbe.org/4l39 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4l39 RCSB], [http://www.ebi.ac.uk/pdbsum/4l39 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4l39 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GH312_ARATH GH312_ARATH]] Catalyzes the conjugation of specific amino acids (e.g. Glu and possibly His, Lys, and Met) to their preferred acyl substrates (e.g. 4-substituted benzoates), in a magnesium ion- and ATP-dependent manner. Can use 4-substituted benzoates such as 4-aminobenzoate (pABA), 4-fluorobenzoate and 4-hydroxybenzoate (4-HBA), and, to a lesser extent, benzoate, vanillate and trans-cinnamate, but not 2-substituted benzoates and salicylic acid (SA), as conjugating acyl substrates. Involved in both basal and induced resistance in a SA-dependent manner. Confers resistance to virulent and avirulent pathogens (at least bacteria and oomycetes), and promotes SA glucosides accumulation. Required for the establishment of hyper-sensitive response (HR) upon incompatible interaction and subsequent systemic acquired resistance (SAR).<ref>PMID:18266921</ref> <ref>PMID:10224270</ref> <ref>PMID:11846877</ref> <ref>PMID:16353557</ref> <ref>PMID:17918621</ref> <ref>PMID:17521413</ref> <ref>PMID:17468220</ref> <ref>PMID:19189963</ref> | + | [https://www.uniprot.org/uniprot/GH312_ARATH GH312_ARATH] Catalyzes the conjugation of specific amino acids (e.g. Glu and possibly His, Lys, and Met) to their preferred acyl substrates (e.g. 4-substituted benzoates), in a magnesium ion- and ATP-dependent manner. Can use 4-substituted benzoates such as 4-aminobenzoate (pABA), 4-fluorobenzoate and 4-hydroxybenzoate (4-HBA), and, to a lesser extent, benzoate, vanillate and trans-cinnamate, but not 2-substituted benzoates and salicylic acid (SA), as conjugating acyl substrates. Involved in both basal and induced resistance in a SA-dependent manner. Confers resistance to virulent and avirulent pathogens (at least bacteria and oomycetes), and promotes SA glucosides accumulation. Required for the establishment of hyper-sensitive response (HR) upon incompatible interaction and subsequent systemic acquired resistance (SAR).<ref>PMID:18266921</ref> <ref>PMID:10224270</ref> <ref>PMID:11846877</ref> <ref>PMID:16353557</ref> <ref>PMID:17918621</ref> <ref>PMID:17521413</ref> <ref>PMID:17468220</ref> <ref>PMID:19189963</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Brown, E]] | + | [[Category: Large Structures]] |
| - | [[Category: Jez, J M]] | + | [[Category: Brown E]] |
| - | [[Category: Kapp, U]] | + | [[Category: Jez JM]] |
| - | [[Category: Marcellin, R]] | + | [[Category: Kapp U]] |
| - | [[Category: Round, A]] | + | [[Category: Marcellin R]] |
| - | [[Category: Westfall, C]] | + | [[Category: Round A]] |
| - | [[Category: Zubieta, C]] | + | [[Category: Westfall C]] |
| - | [[Category: Acyl acid amido synthase]]
| + | [[Category: Zubieta C]] |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Magnesium]]
| + | |
| - | [[Category: Protein-ligand complex]]
| + | |
| Structural highlights
Function
GH312_ARATH Catalyzes the conjugation of specific amino acids (e.g. Glu and possibly His, Lys, and Met) to their preferred acyl substrates (e.g. 4-substituted benzoates), in a magnesium ion- and ATP-dependent manner. Can use 4-substituted benzoates such as 4-aminobenzoate (pABA), 4-fluorobenzoate and 4-hydroxybenzoate (4-HBA), and, to a lesser extent, benzoate, vanillate and trans-cinnamate, but not 2-substituted benzoates and salicylic acid (SA), as conjugating acyl substrates. Involved in both basal and induced resistance in a SA-dependent manner. Confers resistance to virulent and avirulent pathogens (at least bacteria and oomycetes), and promotes SA glucosides accumulation. Required for the establishment of hyper-sensitive response (HR) upon incompatible interaction and subsequent systemic acquired resistance (SAR).[1] [2] [3] [4] [5] [6] [7] [8]
Publication Abstract from PubMed
The combination of protein crystallography and small-angle X-ray scattering (SAXS) provides a powerful method to investigate changes in protein conformation. These complementary structural techniques were used to probe the solution structure of the apo and the ligand-bound forms of the Arabidopsis thaliana acyl acid-amido synthetase GH3.12. This enzyme is part of the extensive GH3 family and plays a critical role in the regulation of plant hormones through the formation of amino-acid-conjugated hormone products via an ATP-dependent reaction mechanism. The enzyme adopts two distinct C-terminal domain orientations with `open' and `closed' active sites. Previous studies suggested that ATP only binds in the open orientation. Here, the X-ray crystal structure of GH3.12 is presented in the closed conformation in complex with the nonhydrolysable ATP analogue AMPCPP and the substrate salicylate. Using on-line HPLC purification combined with SAXS measurements, the most likely apo and ATP-bound protein conformations in solution were determined. These studies demonstrate that the C-terminal domain is flexible in the apo form and favours the closed conformation upon ATP binding. In addition, these data illustrate the efficacy of on-line HPLC purification integrated into the SAXS sample-handling environment to reliably monitor small changes in protein conformation through the collection of aggregate-free and highly redundant data.
Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography.,Round A, Brown E, Marcellin R, Kapp U, Westfall CS, Jez JM, Zubieta C Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):2072-80. doi:, 10.1107/S0907444913019276. Epub 2013 Sep 20. PMID:24100325[9]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lee MW, Jelenska J, Greenberg JT. Arabidopsis proteins important for modulating defense responses to Pseudomonas syringae that secrete HopW1-1. Plant J. 2008 May;54(3):452-65. doi: 10.1111/j.1365-313X.2008.03439.x. Epub 2008 , Feb 7. PMID:18266921 doi:10.1111/j.1365-313X.2008.03439.x
- ↑ Warren RF, Merritt PM, Holub E, Innes RW. Identification of three putative signal transduction genes involved in R gene-specified disease resistance in Arabidopsis. Genetics. 1999 May;152(1):401-12. PMID:10224270
- ↑ van der Biezen EA, Freddie CT, Kahn K, Parker JE, Jones JD. Arabidopsis RPP4 is a member of the RPP5 multigene family of TIR-NB-LRR genes and confers downy mildew resistance through multiple signalling components. Plant J. 2002 Feb;29(4):439-51. PMID:11846877
- ↑ McDowell JM, Williams SG, Funderburg NT, Eulgem T, Dangl JL. Genetic analysis of developmentally regulated resistance to downy mildew (Hyaloperonospora parasitica) in Arabidopsis thaliana. Mol Plant Microbe Interact. 2005 Nov;18(11):1226-34. PMID:16353557 doi:10.1094/MPMI-18-1226
- ↑ Lee MW, Lu H, Jung HW, Greenberg JT. A key role for the Arabidopsis WIN3 protein in disease resistance triggered by Pseudomonas syringae that secrete AvrRpt2. Mol Plant Microbe Interact. 2007 Oct;20(10):1192-200. PMID:17918621 doi:10.1094/MPMI-20-10-1192
- ↑ Jagadeeswaran G, Raina S, Acharya BR, Maqbool SB, Mosher SL, Appel HM, Schultz JC, Klessig DF, Raina R. Arabidopsis GH3-LIKE DEFENSE GENE 1 is required for accumulation of salicylic acid, activation of defense responses and resistance to Pseudomonas syringae. Plant J. 2007 Jul;51(2):234-46. Epub 2007 May 23. PMID:17521413 doi:10.1111/j.1365-313X.2007.03130.x
- ↑ Nobuta K, Okrent RA, Stoutemyer M, Rodibaugh N, Kempema L, Wildermuth MC, Innes RW. The GH3 acyl adenylase family member PBS3 regulates salicylic acid-dependent defense responses in Arabidopsis. Plant Physiol. 2007 Jun;144(2):1144-56. Epub 2007 Apr 27. PMID:17468220 doi:10.1104/pp.107.097691
- ↑ Okrent RA, Brooks MD, Wildermuth MC. Arabidopsis GH3.12 (PBS3) conjugates amino acids to 4-substituted benzoates and is inhibited by salicylate. J Biol Chem. 2009 Apr 10;284(15):9742-54. doi: 10.1074/jbc.M806662200. Epub 2009 , Feb 2. PMID:19189963 doi:10.1074/jbc.M806662200
- ↑ Round A, Brown E, Marcellin R, Kapp U, Westfall CS, Jez JM, Zubieta C. Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography. Acta Crystallogr D Biol Crystallogr. 2013 Oct;69(Pt 10):2072-80. doi:, 10.1107/S0907444913019276. Epub 2013 Sep 20. PMID:24100325 doi:http://dx.doi.org/10.1107/S0907444913019276
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