2z6c

From Proteopedia

(Difference between revisions)

Revision as of 10:46, 8 December 2021

Crystal structure of LOV1 domain of phototropin1 from Arabidopsis thaliana

Structural highlights

2z6c is a 2 chain structure with sequence from Arath. The March 2015 RCSB PDB Molecule of the Month feature on Phototropin by David Goodsell is 10.2210/rcsb_pdb/mom_2015_3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	PHOT1, JK224, NPH1, RPT1 (ARATH)
Activity:	Non-specific serine/threonine protein kinase, with EC number 2.7.11.1
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PHOT1_ARATH] Protein kinase that acts as a blue light photoreceptor in a signal-transduction pathway for photo-induced movements. Required for blue light mediated mRNA destabilization. Mediates calcium spiking of extracellular origin in response to a low rate of blue light. Also mediates rapid membrane depolarization and growth inhibition in response to blue light. Necessary for root phototropism. Involved in hypocotyl phototropism under a low rate but not under a high rate of blue light. Contributes to the chloroplast accumulation but seems not to be required for chloroplast translocation. Regulates stomata opening and photomorphogenesis response of leaf tissue. Confers sensitivity to drought. Not involved in hypocotyl elongation inhibition, anthocyanin accumulation or cotyledon opening.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Phototropin (phot) is a blue-light receptor protein that triggers phototropic responses, chloroplast relocation, and stomata opening to maximize the efficiency of photosynthesis in higher plants. Phot is composed of three functional domains. The N-terminal half folds into two light-oxygen-voltage-sensing domains called LOV1 and LOV2, each binding a flavin mononucleotide to absorb blue light. The C-terminal half is a serine/threonine kinase domain that causes light-dependent autophosphorylation leading to cellular signaling cascades. LOV2 domain is primarily responsible for activation of the kinase, and LOV1 domain is thought to act as a dimerization site and to regulate sensitivity to activation by blue light. Here we show the crystal structures of LOV1 domains of Arabidopsis phot1 and phot2 in the dark at resolutions of 2.1 A and 2.0 A, respectively. Either LOV1 domain forms a dimer through face-to-face association of beta-scaffolds in the crystallographic asymmetric unit. Three types of interactions stabilizing the dimer structures found are as follows: contacts of side chains in their beta-scaffolds, hydrophobic interactions of a short helix found in the N-terminus of a subunit with the beta-scaffolds of both subunits, and hydrogen bonds mediated by hydration water molecules filling the dimer interface. The critical residues for dimerization are Cys261, forming a disulfide bridge between subunits in phot1-LOV1 domain, and Thr217 and Met232 in phot2-LOV1. The topology in homodimeric associations of the LOV1 domains is discussed when referring to those of homodimers or heterodimers of light-oxygen-voltage-sensing or Per-ARNT-Sim domains. The present results also provide clues to understanding structural basis in dimeric interactions of Per-ARNT-Sim protein modules in cellular signaling.

Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2.,Nakasako M, Zikihara K, Matsuoka D, Katsura H, Tokutomi S J Mol Biol. 2008 Sep 5;381(3):718-33. Epub 2008 Jun 18. PMID:18585389^[9]

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

References

↑ Sakai T, Wada T, Ishiguro S, Okada K. RPT2. A signal transducer of the phototropic response in Arabidopsis. Plant Cell. 2000 Feb;12(2):225-36. PMID:10662859
↑ Folta KM, Spalding EP. Unexpected roles for cryptochrome 2 and phototropin revealed by high-resolution analysis of blue light-mediated hypocotyl growth inhibition. Plant J. 2001 Jun;26(5):471-8. PMID:11439133
↑ Folta KM, Kaufman LS. Phototropin 1 is required for high-fluence blue-light-mediated mRNA destabilization. Plant Mol Biol. 2003 Mar;51(4):609-18. PMID:12650626
↑ 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:http://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:http://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
↑ Lariguet P, Schepens I, Hodgson D, Pedmale UV, Trevisan M, Kami C, de Carbonnel M, Alonso JM, Ecker JR, Liscum E, Fankhauser C. PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism. Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):10134-9. Epub 2006 Jun 15. PMID:16777956 doi:http://dx.doi.org/10.1073/pnas.0603799103
↑ Sullivan S, Thomson CE, Lamont DJ, Jones MA, Christie JM. In vivo phosphorylation site mapping and functional characterization of Arabidopsis phototropin 1. Mol Plant. 2008 Jan;1(1):178-94. doi: 10.1093/mp/ssm017. Epub 2007 Dec 4. PMID:20031924 doi:http://dx.doi.org/10.1093/mp/ssm017
↑ Nakasako M, Zikihara K, Matsuoka D, Katsura H, Tokutomi S. Structural basis of the LOV1 dimerization of Arabidopsis phototropins 1 and 2. J Mol Biol. 2008 Sep 5;381(3):718-33. Epub 2008 Jun 18. PMID:18585389 doi:10.1016/j.jmb.2008.06.033

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2z6c"

@@ Line 1: / Line 1: @@
 ==Crystal structure of LOV1 domain of phototropin1 from Arabidopsis thaliana==
-<StructureSection load='2z6c' size='340' side='right' caption='[[2z6c]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='2z6c' size='340' side='right'caption='[[2z6c]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2z6c]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. The March 2015 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Phototropin''  by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2015_3 10.2210/rcsb_pdb/mom_2015_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z6C FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2z6c]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. The March 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Phototropin''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_3 10.2210/rcsb_pdb/mom_2015_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z6C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z6C FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
+</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PHOT1, JK224, NPH1, RPT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PHOT1, JK224, NPH1, RPT1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [https://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6c OCA], [http://pdbe.org/2z6c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z6c RCSB], [http://www.ebi.ac.uk/pdbsum/2z6c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z6c 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=2z6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z6c OCA], [https://pdbe.org/2z6c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z6c RCSB], [https://www.ebi.ac.uk/pdbsum/2z6c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z6c ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PHOT1_ARATH PHOT1_ARATH]] Protein kinase that acts as a blue light photoreceptor in a signal-transduction pathway for photo-induced movements. Required for blue light mediated mRNA destabilization. Mediates calcium spiking of extracellular origin in response to a low rate of blue light. Also mediates rapid membrane depolarization and growth inhibition in response to blue light. Necessary for root phototropism. Involved in hypocotyl phototropism under a low rate but not under a high rate of blue light. Contributes to the chloroplast accumulation but seems not to be required for chloroplast translocation. Regulates stomata opening and photomorphogenesis response of leaf tissue. Confers sensitivity to drought. Not involved in hypocotyl elongation inhibition, anthocyanin accumulation or cotyledon opening.<ref>PMID:10662859</ref> <ref>PMID:11439133</ref> <ref>PMID:12650626</ref> <ref>PMID:12821778</ref> <ref>PMID:15031408</ref> <ref>PMID:14982991</ref> <ref>PMID:16777956</ref> <ref>PMID:20031924</ref>
+[[https://www.uniprot.org/uniprot/PHOT1_ARATH PHOT1_ARATH]] Protein kinase that acts as a blue light photoreceptor in a signal-transduction pathway for photo-induced movements. Required for blue light mediated mRNA destabilization. Mediates calcium spiking of extracellular origin in response to a low rate of blue light. Also mediates rapid membrane depolarization and growth inhibition in response to blue light. Necessary for root phototropism. Involved in hypocotyl phototropism under a low rate but not under a high rate of blue light. Contributes to the chloroplast accumulation but seems not to be required for chloroplast translocation. Regulates stomata opening and photomorphogenesis response of leaf tissue. Confers sensitivity to drought. Not involved in hypocotyl elongation inhibition, anthocyanin accumulation or cotyledon opening.<ref>PMID:10662859</ref> <ref>PMID:11439133</ref> <ref>PMID:12650626</ref> <ref>PMID:12821778</ref> <ref>PMID:15031408</ref> <ref>PMID:14982991</ref> <ref>PMID:16777956</ref> <ref>PMID:20031924</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 35: @@
 </StructureSection>
 [[Category: Arath]]
+[[Category: Large Structures]]
 [[Category: Non-specific serine/threonine protein kinase]]
 [[Category: Phototropin]]

2z6c

From Proteopedia

Revision as of 10:46, 8 December 2021

Crystal structure of LOV1 domain of phototropin1 from Arabidopsis thaliana

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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