6s46: Difference between revisions

Revision as of 12:35, 24 January 2024

Room temperature structure of the LOV2 domain of phototropin-2 from Arabidopsis thaliana 4158 ms after initiation of illumination, determined with a serial crystallography approach

Structural highlights

6s46 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 2.75Å
Ligands:	FMN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHOT2_ARATH Protein kinase that acts as a blue light photoreceptor in a signal-transduction pathway for photo-induced movements. Mediates calcium spiking of extra- and intracellular origins in response to blue light. Involved in hypocotyl phototropism. Contributes to the chloroplast accumulation in low blue light and mediates their translocation (avoidance response) at high fluence. Regulates stomata opening and photomorphogenesis response of leaf tissue. Not involved in hypocotyl elongation inhibition, anthocyanin accumulation or cotyledon opening.^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The recent development of serial crystallography has popularized time-resolved crystallography as a technique to determine the structure of protein-reaction intermediate states. However, most approaches rely on the availability of thousands to millions of microcrystals. A method is reported here, using monochromatic synchrotron radiation, for the room-temperature collection, processing and merging of X-ray oscillation diffraction data from <100 samples in order to observe the build up of a photoreaction intermediate species. Using this method, we monitored with a time resolution of 63 ms how the population of a blue-light photoreceptor domain in a crystal progressively photoconverts from the dark to the light state. The series of resulting snapshots allows us to visualize in detail the gradual rearrangement of both the protein and chromophore during this process.

Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron.,Aumonier S, Santoni G, Gotthard G, von Stetten D, Leonard GA, Royant A IUCrJ. 2020 Jun 24;7(Pt 4):728-736. doi: 10.1107/S2052252520007411. eCollection, 2020 Jul 1. PMID:32695419^[6]

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

References

↑ Sakai T, Kagawa T, Kasahara M, Swartz TE, Christie JM, Briggs WR, Wada M, Okada K. Arabidopsis nph1 and npl1: blue light receptors that mediate both phototropism and chloroplast relocation. Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6969-74. Epub 2001 May 22. PMID:11371609 doi:https://dx.doi.org/10.1073/pnas.101137598
↑ Kagawa T, Sakai T, Suetsugu N, Oikawa K, Ishiguro S, Kato T, Tabata S, Okada K, Wada M. Arabidopsis NPL1: a phototropin homolog controlling the chloroplast high-light avoidance response. Science. 2001 Mar 16;291(5511):2138-41. PMID:11251116 doi:https://dx.doi.org/10.1126/science.291.5511.2138
↑ Harada A, Sakai T, Okada K. Phot1 and phot2 mediate blue light-induced transient increases in cytosolic Ca2+ differently in Arabidopsis leaves. Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8583-8. Epub 2003 Jun 23. PMID:12821778 doi:https://dx.doi.org/10.1073/pnas.1336802100
↑ Inada S, Ohgishi M, Mayama T, Okada K, Sakai T. RPT2 is a signal transducer involved in phototropic response and stomatal opening by association with phototropin 1 in Arabidopsis thaliana. Plant Cell. 2004 Apr;16(4):887-96. Epub 2004 Mar 18. PMID:15031408 doi:https://dx.doi.org/10.1105/tpc.019901
↑ Ohgishi M, Saji K, Okada K, Sakai T. Functional analysis of each blue light receptor, cry1, cry2, phot1, and phot2, by using combinatorial multiple mutants in Arabidopsis. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2223-8. PMID:14982991
↑ Aumonier S, Santoni G, Gotthard G, von Stetten D, Leonard GA, Royant A. Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron. IUCrJ. 2020 Jun 24;7(Pt 4):728-736. doi: 10.1107/S2052252520007411. eCollection, 2020 Jul 1. PMID:32695419 doi:https://dx.doi.org/10.1107/S2052252520007411

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Sakai T, Kagawa T, Kasahara M, Swartz TE, Christie JM, Briggs WR, Wada M, Okada K. Arabidopsis nph1 and npl1: blue light receptors that mediate both phototropism and chloroplast relocation. Proc Natl Acad Sci U S A. 2001 Jun 5;98(12):6969-74. Epub 2001 May 22. PMID:11371609 doi:https://dx.doi.org/10.1073/pnas.101137598

[2] Kagawa T, Sakai T, Suetsugu N, Oikawa K, Ishiguro S, Kato T, Tabata S, Okada K, Wada M. Arabidopsis NPL1: a phototropin homolog controlling the chloroplast high-light avoidance response. Science. 2001 Mar 16;291(5511):2138-41. PMID:11251116 doi:https://dx.doi.org/10.1126/science.291.5511.2138

[3] Harada A, Sakai T, Okada K. Phot1 and phot2 mediate blue light-induced transient increases in cytosolic Ca2+ differently in Arabidopsis leaves. Proc Natl Acad Sci U S A. 2003 Jul 8;100(14):8583-8. Epub 2003 Jun 23. PMID:12821778 doi:https://dx.doi.org/10.1073/pnas.1336802100

[4] Inada S, Ohgishi M, Mayama T, Okada K, Sakai T. RPT2 is a signal transducer involved in phototropic response and stomatal opening by association with phototropin 1 in Arabidopsis thaliana. Plant Cell. 2004 Apr;16(4):887-96. Epub 2004 Mar 18. PMID:15031408 doi:https://dx.doi.org/10.1105/tpc.019901

[5] Ohgishi M, Saji K, Okada K, Sakai T. Functional analysis of each blue light receptor, cry1, cry2, phot1, and phot2, by using combinatorial multiple mutants in Arabidopsis. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2223-8. PMID:14982991

[6] Aumonier S, Santoni G, Gotthard G, von Stetten D, Leonard GA, Royant A. Millisecond time-resolved serial oscillation crystallography of a blue-light photoreceptor at a synchrotron. IUCrJ. 2020 Jun 24;7(Pt 4):728-736. doi: 10.1107/S2052252520007411. eCollection, 2020 Jul 1. PMID:32695419 doi:https://dx.doi.org/10.1107/S2052252520007411

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[5]

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@@ Line 3: / Line 3: @@
 <StructureSection load='6s46' size='340' side='right'caption='[[6s46]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6s46]] is a 1 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=6S46 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6S46 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6s46]] 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=6S46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S46 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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]] 2.75&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PHOT2, CAV1, KIN7, NPL1, At5g58140, K21L19.6 ([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=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=6s46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s46 OCA], [https://pdbe.org/6s46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s46 RCSB], [https://www.ebi.ac.uk/pdbsum/6s46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s46 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6s46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s46 OCA], [http://pdbe.org/6s46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s46 RCSB], [http://www.ebi.ac.uk/pdbsum/6s46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s46 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PHOT2_ARATH PHOT2_ARATH]] Protein kinase that acts as a blue light photoreceptor in a signal-transduction pathway for photo-induced movements. Mediates calcium spiking of extra- and intracellular origins in response to blue light. Involved in hypocotyl phototropism. Contributes to the chloroplast accumulation in low blue light and mediates their translocation (avoidance response) at high fluence. Regulates stomata opening and photomorphogenesis response of leaf tissue. Not involved in hypocotyl elongation inhibition, anthocyanin accumulation or cotyledon opening.<ref>PMID:11371609</ref> <ref>PMID:11251116</ref> <ref>PMID:12821778</ref> <ref>PMID:15031408</ref> <ref>PMID:14982991</ref>
+[https://www.uniprot.org/uniprot/PHOT2_ARATH PHOT2_ARATH] Protein kinase that acts as a blue light photoreceptor in a signal-transduction pathway for photo-induced movements. Mediates calcium spiking of extra- and intracellular origins in response to blue light. Involved in hypocotyl phototropism. Contributes to the chloroplast accumulation in low blue light and mediates their translocation (avoidance response) at high fluence. Regulates stomata opening and photomorphogenesis response of leaf tissue. Not involved in hypocotyl elongation inhibition, anthocyanin accumulation or cotyledon opening.<ref>PMID:11371609</ref> <ref>PMID:11251116</ref> <ref>PMID:12821778</ref> <ref>PMID:15031408</ref> <ref>PMID:14982991</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Non-specific serine/threonine protein kinase]]
+[[Category: Aumonier S]]
-[[Category: Aumonier, S]]
+[[Category: Gotthard G]]
-[[Category: Gotthard, G]]
+[[Category: Leonard G]]
-[[Category: Leonard, G]]
+[[Category: Royant A]]
-[[Category: Royant, A]]
+[[Category: Santoni G]]
-[[Category: Santoni, G]]
+[[Category: Von Stetten D]]
-[[Category: Stetten, D von]]
-[[Category: Flavoprotein]]
-[[Category: Lov domain]]
-[[Category: Photoactive protein]]
-[[Category: Plant protein]]
-[[Category: Time-resolved crystallography]]

6s46: Difference between revisions

Revision as of 12:35, 24 January 2024

Room temperature structure of the LOV2 domain of phototropin-2 from Arabidopsis thaliana 4158 ms after initiation of illumination, determined with a serial crystallography approach

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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