4epl: Difference between revisions

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New page: '''Unreleased structure''' The entry 4epl is ON HOLD Authors: Westfall, C.S., Zubieta, C., Herrmann, J., Kapp, U., Nanao, M.H., Jez, J.M. Description: Crystal Structure of Arabidopsis ...
 
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'''Unreleased structure'''


The entry 4epl is ON HOLD
==Crystal Structure of Arabidopsis thaliana GH3.11 (JAR1) in Complex with JA-Ile==
 
<StructureSection load='4epl' size='340' side='right'caption='[[4epl]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
Authors: Westfall, C.S., Zubieta, C., Herrmann, J., Kapp, U., Nanao, M.H., Jez, J.M.
== Structural highlights ==
 
<table><tr><td colspan='2'>[[4epl]] is a 1 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=4EPL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4EPL FirstGlance]. <br>
Description: Crystal Structure of Arabidopsis thaliana GH3.11 (JAR1) in Complex with JA-Ile
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.007&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=JAI:N-({(1R,2R)-3-OXO-2-[(2Z)-PENT-2-EN-1-YL]CYCLOPENTYL}ACETYL)-L-ISOLEUCINE'>JAI</scene></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=4epl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4epl OCA], [https://pdbe.org/4epl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4epl RCSB], [https://www.ebi.ac.uk/pdbsum/4epl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4epl ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/JAR1_ARATH JAR1_ARATH] Catalyzes the synthesis of jasmonates-amino acid conjugates by adenylation; can use Ile and, in vitro at least, Val, Leu and Phe as conjugating amino acids on jasmonic acid (JA) and 9,10-dihydro-JA substrates, and to a lower extent, on 3-oxo-2-(2Z-pentenyl)-cyclopentane-1-butyric acid (OPC-4) and 12-hydroxy-JA (12-OH-JA). Can synthesize adenosine 5-tetraphosphate in vitro. Required for the JA-mediated signaling pathway that regulates many developmental and defense mechanisms, including growth root inhibition, vegetative storage proteins (VSPs) accumulation, induced systemic resistance (ISR), response to wounding and herbivores, tolerance to ozone O(3) (probably having a role in lesion containment). Plays an important role in the accumulation of JA-Ile in response to wounding, both locally and systemically; promotes JA responding genes especially in distal part of wounded plants, via the JA-Ile-stimulated degradation of JAZ repressor proteins by the SCF(COI)E3 ubiquitin-protein ligase pathway. Involved in the apoptosis-like programmed cell death (PCD) induced by fungal toxin fumonisin B1-mediated (FB1). Required for volatile compounds (C6-aldehydes and allo-ocimene)-mediated defense activation. Involved in the non-pathogenic rhizobacterium-mediated ISR (defense priming) by P.fluorescens (strains CHAOr and WCS417r) and P.putida LSW17S against infection leaf pathogens such as P.syringae pv. tomato and H.parasitica. Required for the JA-dependent resistance to fungi such as P.irregulare, U.vignae and U.appendiculatus. Necessary to induce systemic resistance against R.solanaceraum and P.syringae pv. tomato with P.oligandrum (a non-pathogenic biocontrol agent) cell wall protein fraction (CWP). Mediates PGIP2 accumulation in response to B.cinerea infection and thus contributes to resistance against this pathogen. Modulates the UV-B alteration of leaves attractiveness to diamondback moths P.xylostella leading to insect oviposition. Involved in the regulation of far-red light influence on development. Seems necessary for the salicylic acid (SA)-mediated, NPR1-independent resistance pathway. May contribute to the chitin-elicited pathway. Contributes to the sensitivity toward F.graminearum.<ref>PMID:10921909</ref> <ref>PMID:11006337</ref> <ref>PMID:11041879</ref> <ref>PMID:11041881</ref> <ref>PMID:11090217</ref> <ref>PMID:11607311</ref> <ref>PMID:12084835</ref> <ref>PMID:12236603</ref> <ref>PMID:12376653</ref> <ref>PMID:12509524</ref> <ref>PMID:12744510</ref> <ref>PMID:12848825</ref> <ref>PMID:14558686</ref> <ref>PMID:15258265</ref> <ref>PMID:15879447</ref> <ref>PMID:16639567</ref> <ref>PMID:17220357</ref> <ref>PMID:17291501</ref> <ref>PMID:17601164</ref> <ref>PMID:18247047</ref> <ref>PMID:19251652</ref> <ref>PMID:19304739</ref> <ref>PMID:19473329</ref> <ref>PMID:20521949</ref> <ref>PMID:9724702</ref> <ref>PMID:9807813</ref>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Herrmann J]]
[[Category: Jez JM]]
[[Category: Kapp U]]
[[Category: Nanao MH]]
[[Category: Westfall CS]]
[[Category: Zubieta C]]

Latest revision as of 14:04, 1 March 2024

Crystal Structure of Arabidopsis thaliana GH3.11 (JAR1) in Complex with JA-IleCrystal Structure of Arabidopsis thaliana GH3.11 (JAR1) in Complex with JA-Ile

Structural highlights

4epl is a 1 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 2.007Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

JAR1_ARATH Catalyzes the synthesis of jasmonates-amino acid conjugates by adenylation; can use Ile and, in vitro at least, Val, Leu and Phe as conjugating amino acids on jasmonic acid (JA) and 9,10-dihydro-JA substrates, and to a lower extent, on 3-oxo-2-(2Z-pentenyl)-cyclopentane-1-butyric acid (OPC-4) and 12-hydroxy-JA (12-OH-JA). Can synthesize adenosine 5-tetraphosphate in vitro. Required for the JA-mediated signaling pathway that regulates many developmental and defense mechanisms, including growth root inhibition, vegetative storage proteins (VSPs) accumulation, induced systemic resistance (ISR), response to wounding and herbivores, tolerance to ozone O(3) (probably having a role in lesion containment). Plays an important role in the accumulation of JA-Ile in response to wounding, both locally and systemically; promotes JA responding genes especially in distal part of wounded plants, via the JA-Ile-stimulated degradation of JAZ repressor proteins by the SCF(COI)E3 ubiquitin-protein ligase pathway. Involved in the apoptosis-like programmed cell death (PCD) induced by fungal toxin fumonisin B1-mediated (FB1). Required for volatile compounds (C6-aldehydes and allo-ocimene)-mediated defense activation. Involved in the non-pathogenic rhizobacterium-mediated ISR (defense priming) by P.fluorescens (strains CHAOr and WCS417r) and P.putida LSW17S against infection leaf pathogens such as P.syringae pv. tomato and H.parasitica. Required for the JA-dependent resistance to fungi such as P.irregulare, U.vignae and U.appendiculatus. Necessary to induce systemic resistance against R.solanaceraum and P.syringae pv. tomato with P.oligandrum (a non-pathogenic biocontrol agent) cell wall protein fraction (CWP). Mediates PGIP2 accumulation in response to B.cinerea infection and thus contributes to resistance against this pathogen. Modulates the UV-B alteration of leaves attractiveness to diamondback moths P.xylostella leading to insect oviposition. Involved in the regulation of far-red light influence on development. Seems necessary for the salicylic acid (SA)-mediated, NPR1-independent resistance pathway. May contribute to the chitin-elicited pathway. Contributes to the sensitivity toward F.graminearum.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26]

References

  1. ↑ Hsieh HL, Okamoto H, Wang M, Ang LH, Matsui M, Goodman H, Deng XW. FIN219, an auxin-regulated gene, defines a link between phytochrome A and the downstream regulator COP1 in light control of Arabidopsis development. Genes Dev. 2000 Aug 1;14(15):1958-70. PMID:10921909
  2. ↑ Rao MV, Lee H, Creelman RA, Mullet JE, Davis KR. Jasmonic acid signaling modulates ozone-induced hypersensitive cell death. Plant Cell. 2000 Sep;12(9):1633-46. PMID:11006337
  3. ↑ Asai T, Stone JM, Heard JE, Kovtun Y, Yorgey P, Sheen J, Ausubel FM. Fumonisin B1-induced cell death in arabidopsis protoplasts requires jasmonate-, ethylene-, and salicylate-dependent signaling pathways. Plant Cell. 2000 Oct;12(10):1823-36. PMID:11041879
  4. ↑ Overmyer K, Tuominen H, Kettunen R, Betz C, Langebartels C, Sandermann H Jr, Kangasjarvi J. Ozone-sensitive arabidopsis rcd1 mutant reveals opposite roles for ethylene and jasmonate signaling pathways in regulating superoxide-dependent cell death. Plant Cell. 2000 Oct;12(10):1849-62. PMID:11041881
  5. ↑ Clarke JD, Volko SM, Ledford H, Ausubel FM, Dong X. Roles of salicylic acid, jasmonic acid, and ethylene in cpr-induced resistance in arabidopsis. Plant Cell. 2000 Nov;12(11):2175-90. PMID:11090217
  6. ↑ Staswick PE, Su W, Howell SH. Methyl jasmonate inhibition of root growth and induction of a leaf protein are decreased in an Arabidopsis thaliana mutant. Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):6837-40. PMID:11607311
  7. ↑ Staswick PE, Tiryaki I, Rowe ML. Jasmonate response locus JAR1 and several related Arabidopsis genes encode enzymes of the firefly luciferase superfamily that show activity on jasmonic, salicylic, and indole-3-acetic acids in an assay for adenylation. Plant Cell. 2002 Jun;14(6):1405-15. PMID:12084835
  8. ↑ Zhang B, Ramonell K, Somerville S, Stacey G. Characterization of early, chitin-induced gene expression in Arabidopsis. Mol Plant Microbe Interact. 2002 Sep;15(9):963-70. PMID:12236603 doi:http://dx.doi.org/10.1094/MPMI.2002.15.9.963
  9. ↑ Tiryaki I, Staswick PE. An Arabidopsis mutant defective in jasmonate response is allelic to the auxin-signaling mutant axr1. Plant Physiol. 2002 Oct;130(2):887-94. PMID:12376653 doi:http://dx.doi.org/10.1104/pp.005272
  10. ↑ Ferrari S, Vairo D, Ausubel FM, Cervone F, De Lorenzo G. Tandemly duplicated Arabidopsis genes that encode polygalacturonase-inhibiting proteins are regulated coordinately by different signal transduction pathways in response to fungal infection. Plant Cell. 2003 Jan;15(1):93-106. PMID:12509524
  11. ↑ Mellersh DG, Heath MC. An investigation into the involvement of defense signaling pathways in components of the nonhost resistance of Arabidopsis thaliana to rust fungi also reveals a model system for studying rust fungal compatibility. Mol Plant Microbe Interact. 2003 May;16(5):398-404. PMID:12744510 doi:http://dx.doi.org/10.1094/MPMI.2003.16.5.398
  12. ↑ Ferrari S, Plotnikova JM, De Lorenzo G, Ausubel FM. Arabidopsis local resistance to Botrytis cinerea involves salicylic acid and camalexin and requires EDS4 and PAD2, but not SID2, EDS5 or PAD4. Plant J. 2003 Jul;35(2):193-205. PMID:12848825
  13. ↑ Iavicoli A, Boutet E, Buchala A, Metraux JP. Induced systemic resistance in Arabidopsis thaliana in response to root inoculation with Pseudomonas fluorescens CHA0. Mol Plant Microbe Interact. 2003 Oct;16(10):851-8. PMID:14558686 doi:http://dx.doi.org/10.1094/MPMI.2003.16.10.851
  14. ↑ Staswick PE, Tiryaki I. The oxylipin signal jasmonic acid is activated by an enzyme that conjugates it to isoleucine in Arabidopsis. Plant Cell. 2004 Aug;16(8):2117-27. Epub 2004 Jul 16. PMID:15258265 doi:http://dx.doi.org/10.1105/tpc.104.023549
  15. ↑ Kishimoto K, Matsui K, Ozawa R, Takabayashi J. Volatile C6-aldehydes and Allo-ocimene activate defense genes and induce resistance against Botrytis cinerea in Arabidopsis thaliana. Plant Cell Physiol. 2005 Jul;46(7):1093-102. Epub 2005 May 6. PMID:15879447 doi:http://dx.doi.org/10.1093/pcp/pci122
  16. ↑ Caputo C, Rutitzky M, Ballare CL. Solar ultraviolet-B radiation alters the attractiveness of Arabidopsis plants to diamondback moths (Plutella xylostella L.): impacts on oviposition and involvement of the jasmonic acid pathway. Oecologia. 2006 Aug;149(1):81-90. Epub 2006 Apr 26. PMID:16639567 doi:http://dx.doi.org/10.1007/s00442-006-0422-3
  17. ↑ Chen IC, Huang IC, Liu MJ, Wang ZG, Chung SS, Hsieh HL. Glutathione S-transferase interacting with far-red insensitive 219 is involved in phytochrome A-mediated signaling in Arabidopsis. Plant Physiol. 2007 Mar;143(3):1189-202. Epub 2007 Jan 12. PMID:17220357 doi:http://dx.doi.org/10.1104/pp.106.094185
  18. ↑ Guranowski A, Miersch O, Staswick PE, Suza W, Wasternack C. Substrate specificity and products of side-reactions catalyzed by jasmonate:amino acid synthetase (JAR1). FEBS Lett. 2007 Mar 6;581(5):815-20. Epub 2007 Feb 2. PMID:17291501 doi:http://dx.doi.org/10.1016/j.febslet.2007.01.049
  19. ↑ Ahn IP, Lee SW, Suh SC. Rhizobacteria-induced priming in Arabidopsis is dependent on ethylene, jasmonic acid, and NPR1. Mol Plant Microbe Interact. 2007 Jul;20(7):759-68. PMID:17601164 doi:http://dx.doi.org/10.1094/MPMI-20-7-0759
  20. ↑ Suza WP, Staswick PE. The role of JAR1 in Jasmonoyl-L: -isoleucine production during Arabidopsis wound response. Planta. 2008 May;227(6):1221-32. doi: 10.1007/s00425-008-0694-4. Epub 2008 Feb 5. PMID:18247047 doi:http://dx.doi.org/10.1007/s00425-008-0694-4
  21. ↑ Moreno JE, Tao Y, Chory J, Ballare CL. Ecological modulation of plant defense via phytochrome control of jasmonate sensitivity. Proc Natl Acad Sci U S A. 2009 Mar 24;106(12):4935-40. doi:, 10.1073/pnas.0900701106. Epub 2009 Feb 27. PMID:19251652 doi:http://dx.doi.org/10.1073/pnas.0900701106
  22. ↑ Kawamura Y, Takenaka S, Hase S, Kubota M, Ichinose Y, Kanayama Y, Nakaho K, Klessig DF, Takahashi H. Enhanced defense responses in Arabidopsis induced by the cell wall protein fractions from Pythium oligandrum require SGT1, RAR1, NPR1 and JAR1. Plant Cell Physiol. 2009 May;50(5):924-34. doi: 10.1093/pcp/pcp044. Epub 2009 Mar, 20. PMID:19304739 doi:http://dx.doi.org/10.1093/pcp/pcp044
  23. ↑ Koo AJ, Gao X, Jones AD, Howe GA. A rapid wound signal activates the systemic synthesis of bioactive jasmonates in Arabidopsis. Plant J. 2009 Sep;59(6):974-86. doi: 10.1111/j.1365-313X.2009.03924.x. Epub 2009 , May 18. PMID:19473329 doi:http://dx.doi.org/10.1111/j.1365-313X.2009.03924.x
  24. ↑ Makandar R, Nalam V, Chaturvedi R, Jeannotte R, Sparks AA, Shah J. Involvement of salicylate and jasmonate signaling pathways in Arabidopsis interaction with Fusarium graminearum. Mol Plant Microbe Interact. 2010 Jul;23(7):861-70. doi: 10.1094/MPMI-23-7-0861. PMID:20521949 doi:http://dx.doi.org/10.1094/MPMI-23-7-0861
  25. ↑ Pieterse CM, van Wees SC, van Pelt JA, Knoester M, Laan R, Gerrits H, Weisbeek PJ, van Loon LC. A novel signaling pathway controlling induced systemic resistance in Arabidopsis. Plant Cell. 1998 Sep;10(9):1571-80. PMID:9724702
  26. ↑ Staswick PE, Yuen GY, Lehman CC. Jasmonate signaling mutants of Arabidopsis are susceptible to the soil fungus Pythium irregulare. Plant J. 1998 Sep;15(6):747-54. PMID:9807813

4epl, resolution 2.01Å

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