6kz9: Difference between revisions

Latest revision as of 10:44, 27 March 2024

Crystal structure of plant Phospholipase D alpha

Structural highlights

6kz9 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 1.801Å
Ligands:	CA
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PLDA1_ARATH Hydrolyzes glycerol-phospholipids at the terminal phosphodiesteric bond to generate phosphatidic acids (PA). Plays an important role in various cellular processes, including phytohormone action and response to stress, characterized by acidification of the cell (PubMed:9437863). Involved in wound induction of jasmonic acid (PubMed:11090221). May be involved in membrane lipid remodeling (PubMed:11239826). Probably involved in freezing tolerance by modulating the cold-responsive genes and accumulation of osmolytes (PubMed:16949955). Can use phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as substrates, both in presence or in absence of PIP2 (PubMed:9578608). Its main substrate is phosphatidylcholine (PubMed:11239826). Stimulates the intrinsic GTPase activity of GPA1 upon binding (PubMed:14594812). Mediates the abscisic acid effects on stomata through interaction with GPA1 and the production of phosphatidic acid that bind to ABI1 (PubMed:17261695, PubMed:17565616). Involved in seed aging and deterioration (PubMed:17565616). Involved in microtubule stabilization and salt tolerance (PubMed:23150630). Involved in abscisic acid-induced stomatal closure (PubMed:22392280).^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12]

References

↑ Pappan K, Wang X. Plant phospholipase Dalpha is an acidic phospholipase active at near-physiological Ca(2+) concentrations. Arch Biochem Biophys. 1999 Aug 15;368(2):347-53. doi: 10.1006/abbi.1999.1325. PMID:10441386 doi:https://dx.doi.org/10.1006/abbi.1999.1325
↑ Wang C, Zien CA, Afitlhile M, Welti R, Hildebrand DF, Wang X. Involvement of phospholipase D in wound-induced accumulation of jasmonic acid in arabidopsis. Plant Cell. 2000 Nov;12(11):2237-46. doi: 10.1105/tpc.12.11.2237. PMID:11090221 doi:https://dx.doi.org/10.1105/tpc.12.11.2237
↑ Zien CA, Wang C, Wang X, Welti R. In vivo substrates and the contribution of the common phospholipase D, PLDalpha, to wound-induced metabolism of lipids in Arabidopsis. Biochim Biophys Acta. 2001 Feb 26;1530(2-3):236-48. doi:, 10.1016/s1388-1981(01)00091-9. PMID:11239826 doi:https://dx.doi.org/10.1016/s1388-1981(01)00091-9
↑ Zhao J, Wang X. Arabidopsis phospholipase Dalpha1 interacts with the heterotrimeric G-protein alpha-subunit through a motif analogous to the DRY motif in G-protein-coupled receptors. J Biol Chem. 2004 Jan 16;279(3):1794-800. doi: 10.1074/jbc.M309529200. Epub 2003 , Oct 31. PMID:14594812 doi:https://dx.doi.org/10.1074/jbc.M309529200
↑ Mishra G, Zhang W, Deng F, Zhao J, Wang X. A bifurcating pathway directs abscisic acid effects on stomatal closure and opening in Arabidopsis. Science. 2006 Apr 14;312(5771):264-6. PMID:16614222 doi:312/5771/264
↑ Rajashekar CB, Zhou HE, Zhang Y, Li W, Wang X. Suppression of phospholipase Dalpha1 induces freezing tolerance in Arabidopsis: response of cold-responsive genes and osmolyte accumulation. J Plant Physiol. 2006 Sep;163(9):916-26. doi: 10.1016/j.jplph.2005.08.006. Epub, 2005 Oct 5. PMID:16949955 doi:https://dx.doi.org/10.1016/j.jplph.2005.08.006
↑ Mane SP, Vasquez-Robinet C, Sioson AA, Heath LS, Grene R. Early PLDalpha-mediated events in response to progressive drought stress in Arabidopsis: a transcriptome analysis. J Exp Bot. 2007;58(2):241-52. doi: 10.1093/jxb/erl262. PMID:17261695 doi:https://dx.doi.org/10.1093/jxb/erl262
↑ Devaiah SP, Pan X, Hong Y, Roth M, Welti R, Wang X. Enhancing seed quality and viability by suppressing phospholipase D in Arabidopsis. Plant J. 2007 Jun;50(6):950-7. doi: 10.1111/j.1365-313X.2007.03103.x. PMID:17565616 doi:https://dx.doi.org/10.1111/j.1365-313X.2007.03103.x
↑ Uraji M, Katagiri T, Okuma E, Ye W, Hossain MA, Masuda C, Miura A, Nakamura Y, Mori IC, Shinozaki K, Murata Y. Cooperative function of PLDdelta and PLDalpha1 in abscisic acid-induced stomatal closure in Arabidopsis. Plant Physiol. 2012 May;159(1):450-60. doi: 10.1104/pp.112.195578. Epub 2012 Mar , 5. PMID:22392280 doi:https://dx.doi.org/10.1104/pp.112.195578
↑ Zhang Q, Lin F, Mao T, Nie J, Yan M, Yuan M, Zhang W. Phosphatidic acid regulates microtubule organization by interacting with MAP65-1 in response to salt stress in Arabidopsis. Plant Cell. 2012 Nov;24(11):4555-76. doi: 10.1105/tpc.112.104182. Epub 2012 Nov, 13. PMID:23150630 doi:https://dx.doi.org/10.1105/tpc.112.104182
↑ Fan L, Zheng S, Wang X. Antisense suppression of phospholipase D alpha retards abscisic acid- and ethylene-promoted senescence of postharvest Arabidopsis leaves. Plant Cell. 1997 Dec;9(12):2183-96. doi: 10.1105/tpc.9.12.2183. PMID:9437863 doi:https://dx.doi.org/10.1105/tpc.9.12.2183
↑ Pappan K, Austin-Brown S, Chapman KD, Wang X. Substrate selectivities and lipid modulation of plant phospholipase D alpha, -beta, and -gamma. Arch Biochem Biophys. 1998 May 1;353(1):131-40. doi: 10.1006/abbi.1998.0640. PMID:9578608 doi:https://dx.doi.org/10.1006/abbi.1998.0640

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OCA

[1] Pappan K, Wang X. Plant phospholipase Dalpha is an acidic phospholipase active at near-physiological Ca(2+) concentrations. Arch Biochem Biophys. 1999 Aug 15;368(2):347-53. doi: 10.1006/abbi.1999.1325. PMID:10441386 doi:https://dx.doi.org/10.1006/abbi.1999.1325

[2] Wang C, Zien CA, Afitlhile M, Welti R, Hildebrand DF, Wang X. Involvement of phospholipase D in wound-induced accumulation of jasmonic acid in arabidopsis. Plant Cell. 2000 Nov;12(11):2237-46. doi: 10.1105/tpc.12.11.2237. PMID:11090221 doi:https://dx.doi.org/10.1105/tpc.12.11.2237

[3] Zien CA, Wang C, Wang X, Welti R. In vivo substrates and the contribution of the common phospholipase D, PLDalpha, to wound-induced metabolism of lipids in Arabidopsis. Biochim Biophys Acta. 2001 Feb 26;1530(2-3):236-48. doi:, 10.1016/s1388-1981(01)00091-9. PMID:11239826 doi:https://dx.doi.org/10.1016/s1388-1981(01)00091-9

[4] Zhao J, Wang X. Arabidopsis phospholipase Dalpha1 interacts with the heterotrimeric G-protein alpha-subunit through a motif analogous to the DRY motif in G-protein-coupled receptors. J Biol Chem. 2004 Jan 16;279(3):1794-800. doi: 10.1074/jbc.M309529200. Epub 2003 , Oct 31. PMID:14594812 doi:https://dx.doi.org/10.1074/jbc.M309529200

[5] Mishra G, Zhang W, Deng F, Zhao J, Wang X. A bifurcating pathway directs abscisic acid effects on stomatal closure and opening in Arabidopsis. Science. 2006 Apr 14;312(5771):264-6. PMID:16614222 doi:312/5771/264

[6] Rajashekar CB, Zhou HE, Zhang Y, Li W, Wang X. Suppression of phospholipase Dalpha1 induces freezing tolerance in Arabidopsis: response of cold-responsive genes and osmolyte accumulation. J Plant Physiol. 2006 Sep;163(9):916-26. doi: 10.1016/j.jplph.2005.08.006. Epub, 2005 Oct 5. PMID:16949955 doi:https://dx.doi.org/10.1016/j.jplph.2005.08.006

[7] Mane SP, Vasquez-Robinet C, Sioson AA, Heath LS, Grene R. Early PLDalpha-mediated events in response to progressive drought stress in Arabidopsis: a transcriptome analysis. J Exp Bot. 2007;58(2):241-52. doi: 10.1093/jxb/erl262. PMID:17261695 doi:https://dx.doi.org/10.1093/jxb/erl262

[8] Devaiah SP, Pan X, Hong Y, Roth M, Welti R, Wang X. Enhancing seed quality and viability by suppressing phospholipase D in Arabidopsis. Plant J. 2007 Jun;50(6):950-7. doi: 10.1111/j.1365-313X.2007.03103.x. PMID:17565616 doi:https://dx.doi.org/10.1111/j.1365-313X.2007.03103.x

[9] Uraji M, Katagiri T, Okuma E, Ye W, Hossain MA, Masuda C, Miura A, Nakamura Y, Mori IC, Shinozaki K, Murata Y. Cooperative function of PLDdelta and PLDalpha1 in abscisic acid-induced stomatal closure in Arabidopsis. Plant Physiol. 2012 May;159(1):450-60. doi: 10.1104/pp.112.195578. Epub 2012 Mar , 5. PMID:22392280 doi:https://dx.doi.org/10.1104/pp.112.195578

[10] Zhang Q, Lin F, Mao T, Nie J, Yan M, Yuan M, Zhang W. Phosphatidic acid regulates microtubule organization by interacting with MAP65-1 in response to salt stress in Arabidopsis. Plant Cell. 2012 Nov;24(11):4555-76. doi: 10.1105/tpc.112.104182. Epub 2012 Nov, 13. PMID:23150630 doi:https://dx.doi.org/10.1105/tpc.112.104182

[11] Fan L, Zheng S, Wang X. Antisense suppression of phospholipase D alpha retards abscisic acid- and ethylene-promoted senescence of postharvest Arabidopsis leaves. Plant Cell. 1997 Dec;9(12):2183-96. doi: 10.1105/tpc.9.12.2183. PMID:9437863 doi:https://dx.doi.org/10.1105/tpc.9.12.2183

[12] Pappan K, Austin-Brown S, Chapman KD, Wang X. Substrate selectivities and lipid modulation of plant phospholipase D alpha, -beta, and -gamma. Arch Biochem Biophys. 1998 May 1;353(1):131-40. doi: 10.1006/abbi.1998.0640. PMID:9578608 doi:https://dx.doi.org/10.1006/abbi.1998.0640

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 6kz9 is ON HOLD
+==Crystal structure of plant Phospholipase D alpha==
+<StructureSection load='6kz9' size='340' side='right'caption='[[6kz9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[6kz9]] 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=6KZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KZ9 FirstGlance]. <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]] 1.801&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=6kz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kz9 OCA], [https://pdbe.org/6kz9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kz9 RCSB], [https://www.ebi.ac.uk/pdbsum/6kz9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kz9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PLDA1_ARATH PLDA1_ARATH] Hydrolyzes glycerol-phospholipids at the terminal phosphodiesteric bond to generate phosphatidic acids (PA). Plays an important role in various cellular processes, including phytohormone action and response to stress, characterized by acidification of the cell (PubMed:9437863). Involved in wound induction of jasmonic acid (PubMed:11090221). May be involved in membrane lipid remodeling (PubMed:11239826). Probably involved in freezing tolerance by modulating the cold-responsive genes and accumulation of osmolytes (PubMed:16949955). Can use phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as substrates, both in presence or in absence of PIP2 (PubMed:9578608). Its main substrate is phosphatidylcholine (PubMed:11239826). Stimulates the intrinsic GTPase activity of GPA1 upon binding (PubMed:14594812). Mediates the abscisic acid effects on stomata through interaction with GPA1 and the production of phosphatidic acid that bind to ABI1 (PubMed:17261695, PubMed:17565616). Involved in seed aging and deterioration (PubMed:17565616). Involved in microtubule stabilization and salt tolerance (PubMed:23150630). Involved in abscisic acid-induced stomatal closure (PubMed:22392280).<ref>PMID:10441386</ref> <ref>PMID:11090221</ref> <ref>PMID:11239826</ref> <ref>PMID:14594812</ref> <ref>PMID:16614222</ref> <ref>PMID:16949955</ref> <ref>PMID:17261695</ref> <ref>PMID:17565616</ref> <ref>PMID:22392280</ref> <ref>PMID:23150630</ref> <ref>PMID:9437863</ref> <ref>PMID:9578608</ref>
-Authors: Li, J.X., Yu, F., Zhang, P.
+==See Also==
+*[[Phospholipase D 3D structures|Phospholipase D 3D structures]]
-Description: Crystal structure of plant PLD alpha
+== References ==
-[[Category: Unreleased Structures]]
+<references/>
-[[Category: Li, J.X]]
+__TOC__
-[[Category: Zhang, P]]
+</StructureSection>
-[[Category: Yu, F]]
+[[Category: Arabidopsis thaliana]]
+[[Category: Large Structures]]
+[[Category: Li JX]]
+[[Category: Yu F]]
+[[Category: Zhang P]]

6kz9: Difference between revisions

Latest revision as of 10:44, 27 March 2024

Crystal structure of plant Phospholipase D alpha

Structural highlights

Function

See Also

References

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