6gre: Difference between revisions

Latest revision as of 12:41, 6 November 2024

Crystal structure of the tandem DUF26 ectodomain from the Arabidopsis thaliana cysteine-rich receptor-like protein PDLP5.

Structural highlights

6gre 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 1.29Å
Ligands:	AE3, EDO, GOL, NA, NAG, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PDLP5_ARATH Modulates cell-to-cell trafficking. Has a positive role in innate immunity. Required for systemic acquired resistance (SAR) which is mediated by the signaling molecules azelaic acid (AzA), glycerol-3-phosphate (G3P), and salicylic acid (SA) (PubMed:27078071). Negative regulator of plasmodesmata permeability triggered by SA during immune responses, through regulation of callose deposition (PubMed:21934146, PubMed:23749844). Delays the trafficking of Tobacco Mosaic Virus (TMV) movement protein (MP). Required for symplastic signal transport (PubMed:27078071).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation. However, gene and genome duplications pose difficulties for functional characterization and translational research. Here we infer the evolutionary history of the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 emerged in secreted proteins. Domain duplications and rearrangements led to the appearance of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). The DUF26 is land plant-specific but structural analyses of PDLP ectodomains revealed strong similarity to fungal lectins and thus may constitute a group of plant carbohydrate-binding proteins. CRKs expanded through tandem duplications and preferential retention of duplicates following whole genome duplications, whereas PDLPs evolved according to the dosage balance hypothesis. We propose that new gene families mainly expand through small-scale duplications, while fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.

Mechanistic insights into the evolution of DUF26-containing proteins in land plants.,Vaattovaara A, Brandt B, Rajaraman S, Safronov O, Veidenberg A, Luklova M, Kangasjarvi J, Loytynoja A, Hothorn M, Salojarvi J, Wrzaczek M Commun Biol. 2019 Feb 8;2:56. doi: 10.1038/s42003-019-0306-9. eCollection 2019. PMID:30775457^[4]

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

References

↑ Lee JY, Wang X, Cui W, Sager R, Modla S, Czymmek K, Zybaliov B, van Wijk K, Zhang C, Lu H, Lakshmanan V. A plasmodesmata-localized protein mediates crosstalk between cell-to-cell communication and innate immunity in Arabidopsis. Plant Cell. 2011 Sep;23(9):3353-73. doi: 10.1105/tpc.111.087742. Epub 2011 Sep, 20. PMID:21934146 doi:https://dx.doi.org/10.1105/tpc.111.087742
↑ Wang X, Sager R, Cui W, Zhang C, Lu H, Lee JY. Salicylic acid regulates Plasmodesmata closure during innate immune responses in Arabidopsis. Plant Cell. 2013 Jun;25(6):2315-29. doi: 10.1105/tpc.113.110676. Epub 2013 Jun 7. PMID:23749844 doi:https://dx.doi.org/10.1105/tpc.113.110676
↑ Lim GH, Shine MB, de Lorenzo L, Yu K, Cui W, Navarre D, Hunt AG, Lee JY, Kachroo A, Kachroo P. Plasmodesmata Localizing Proteins Regulate Transport and Signaling during Systemic Acquired Immunity in Plants. Cell Host Microbe. 2016 Apr 13;19(4):541-9. PMID:27078071 doi:10.1016/j.chom.2016.03.006
↑ Vaattovaara A, Brandt B, Rajaraman S, Safronov O, Veidenberg A, Luklova M, Kangasjarvi J, Loytynoja A, Hothorn M, Salojarvi J, Wrzaczek M. Mechanistic insights into the evolution of DUF26-containing proteins in land plants. Commun Biol. 2019 Feb 8;2:56. doi: 10.1038/s42003-019-0306-9. eCollection 2019. PMID:30775457 doi:https://dx.doi.org/10.1038/s42003-019-0306-9

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OCA

[1] Lee JY, Wang X, Cui W, Sager R, Modla S, Czymmek K, Zybaliov B, van Wijk K, Zhang C, Lu H, Lakshmanan V. A plasmodesmata-localized protein mediates crosstalk between cell-to-cell communication and innate immunity in Arabidopsis. Plant Cell. 2011 Sep;23(9):3353-73. doi: 10.1105/tpc.111.087742. Epub 2011 Sep, 20. PMID:21934146 doi:https://dx.doi.org/10.1105/tpc.111.087742

[2] Wang X, Sager R, Cui W, Zhang C, Lu H, Lee JY. Salicylic acid regulates Plasmodesmata closure during innate immune responses in Arabidopsis. Plant Cell. 2013 Jun;25(6):2315-29. doi: 10.1105/tpc.113.110676. Epub 2013 Jun 7. PMID:23749844 doi:https://dx.doi.org/10.1105/tpc.113.110676

[3] Lim GH, Shine MB, de Lorenzo L, Yu K, Cui W, Navarre D, Hunt AG, Lee JY, Kachroo A, Kachroo P. Plasmodesmata Localizing Proteins Regulate Transport and Signaling during Systemic Acquired Immunity in Plants. Cell Host Microbe. 2016 Apr 13;19(4):541-9. PMID:27078071 doi:10.1016/j.chom.2016.03.006

[4] Vaattovaara A, Brandt B, Rajaraman S, Safronov O, Veidenberg A, Luklova M, Kangasjarvi J, Loytynoja A, Hothorn M, Salojarvi J, Wrzaczek M. Mechanistic insights into the evolution of DUF26-containing proteins in land plants. Commun Biol. 2019 Feb 8;2:56. doi: 10.1038/s42003-019-0306-9. eCollection 2019. PMID:30775457 doi:https://dx.doi.org/10.1038/s42003-019-0306-9

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==Crystal structure of the tandem DUF26 ectodomain from the Arabidopsis thaliana cysteine-rich receptor-like protein PDLP5.==
-<StructureSection load='6gre' size='340' side='right' caption='[[6gre]], [[Resolution|resolution]] 1.29&Aring;' scene=''>
+<StructureSection load='6gre' size='340' side='right'caption='[[6gre]], [[Resolution|resolution]] 1.29&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6gre]] 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=6GRE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GRE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6gre]] 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=6GRE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GRE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AE3:2-(2-ETHOXYETHOXY)ETHANOL'>AE3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.29&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CRRSP2, HWI1, At1g70690, F5A18.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AE3:2-(2-ETHOXYETHOXY)ETHANOL'>AE3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=6gre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gre OCA], [http://pdbe.org/6gre PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gre RCSB], [http://www.ebi.ac.uk/pdbsum/6gre PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gre ProSAT]</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=6gre FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gre OCA], [https://pdbe.org/6gre PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6gre RCSB], [https://www.ebi.ac.uk/pdbsum/6gre PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6gre ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CRRS2_ARATH CRRS2_ARATH]] Modulates cell-to-cell trafficking. Has a positive role in innate immunity. Negative regulator of plasmodesmata permeability triggered by salicylic acid during immune responses, through regulation of callose deposition. Delays the trafficking of Tobacco Mosaic Virus (TMV) movement protein (MP).<ref>PMID:21934146</ref> <ref>PMID:23749844</ref>
+[https://www.uniprot.org/uniprot/PDLP5_ARATH PDLP5_ARATH] Modulates cell-to-cell trafficking. Has a positive role in innate immunity. Required for systemic acquired resistance (SAR) which is mediated by the signaling molecules azelaic acid (AzA), glycerol-3-phosphate (G3P), and salicylic acid (SA) (PubMed:27078071). Negative regulator of plasmodesmata permeability triggered by SA during immune responses, through regulation of callose deposition (PubMed:21934146, PubMed:23749844). Delays the trafficking of Tobacco Mosaic Virus (TMV) movement protein (MP). Required for symplastic signal transport (PubMed:27078071).<ref>PMID:21934146</ref> <ref>PMID:23749844</ref> <ref>PMID:27078071</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Brandt, B]]
+[[Category: Large Structures]]
-[[Category: Hothorn, M]]
+[[Category: Brandt B]]
-[[Category: Disulfide bond]]
+[[Category: Hothorn M]]
-[[Category: Duf26 domain]]
-[[Category: Immune signaling]]
-[[Category: Lectin]]
-[[Category: Membrane protein]]
-[[Category: Plasmodesmata]]
-[[Category: Signaling protein]]

6gre: Difference between revisions

Latest revision as of 12:41, 6 November 2024

Crystal structure of the tandem DUF26 ectodomain from the Arabidopsis thaliana cysteine-rich receptor-like protein PDLP5.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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