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4our

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Crystal structure of Arabidopsis thaliana phytochrome B photosensory module

Structural highlights

4our 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 3.4Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PHYB_ARATH Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region. Photoconversion of Pr to Pfr induces an array of morphogenetic responses, whereas reconversion of Pfr to Pr cancels the induction of those responses. Pfr controls the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase, rRNA, etc. It also controls the expression of its own gene(s) in a negative feedback fashion. Involved in the flowering time regulation.^[1] ^[2]

Publication Abstract from PubMed

Many aspects of plant photomorphogenesis are controlled by the phytochrome (Phy) family of bilin-containing photoreceptors that detect red and far-red light by photointerconversion between a dark-adapted Pr state and a photoactivated Pfr state. Whereas 3D models of prokaryotic Phys are available, models of their plant counterparts have remained elusive. Here, we present the crystal structure of the photosensing module (PSM) from a seed plant Phy in the Pr state using the PhyB isoform from Arabidopsis thaliana. The PhyB PSM crystallized as a head-to-head dimer with strong structural homology to its bacterial relatives, including a 5(Z)syn, 10(Z)syn, 15(Z)anti configuration of the phytochromobilin chromophore buried within the cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) domain, and a well-ordered hairpin protruding from the Phy-specific domain toward the bilin pocket. However, its Per/Arnt/Sim (PAS) domain, knot region, and helical spine show distinct structural differences potentially important to signaling. Included is an elongated helical spine, an extended beta-sheet connecting the GAF domain and hairpin stem, and unique interactions between the region upstream of the PAS domain knot and the bilin A and B pyrrole rings. Comparisons of this structure with those from bacterial Phys combined with mutagenic studies support a toggle model for photoconversion that engages multiple features within the PSM to stabilize the Pr and Pfr end states after rotation of the D pyrrole ring. Taken together, this Arabidopsis PhyB structure should enable molecular insights into plant Phy signaling and provide an essential scaffold to redesign their activities for agricultural benefit and as optogenetic reagents.

Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome.,Burgie ES, Bussell AN, Walker JM, Dubiel K, Vierstra RD Proc Natl Acad Sci U S A. 2014 Jun 30. pii: 201403096. PMID:24982198^[3]

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

References

↑ Kim DH, Kang JG, Yang SS, Chung KS, Song PS, Park CM. A phytochrome-associated protein phosphatase 2A modulates light signals in flowering time control in Arabidopsis. Plant Cell. 2002 Dec;14(12):3043-56. PMID:12468726
↑ Ryu JS, Kim JI, Kunkel T, Kim BC, Cho DS, Hong SH, Kim SH, Fernandez AP, Kim Y, Alonso JM, Ecker JR, Nagy F, Lim PO, Song PS, Schafer E, Nam HG. Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer. Cell. 2005 Feb 11;120(3):395-406. PMID:15707897 doi:http://dx.doi.org/10.1016/j.cell.2004.12.019
↑ Burgie ES, Bussell AN, Walker JM, Dubiel K, Vierstra RD. Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Proc Natl Acad Sci U S A. 2014 Jun 30. pii: 201403096. PMID:24982198 doi:http://dx.doi.org/10.1073/pnas.1403096111

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4our"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Arabidopsis thaliana phytochrome B photosensory module==
-<StructureSection load='4our' size='340' side='right' caption='[[4our]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
+<StructureSection load='4our' size='340' side='right'caption='[[4our]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4our]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OUR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OUR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4our]] 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=4OUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OUR FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2VO:PHYTOCHROMOBILIN,+BOUND+FORM'>2VO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><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]] 3.4&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=O6E:3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic+acid'>O6E</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4our FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4our OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4our RCSB], [http://www.ebi.ac.uk/pdbsum/4our PDBsum]</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=4our FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4our OCA], [https://pdbe.org/4our PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4our RCSB], [https://www.ebi.ac.uk/pdbsum/4our PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4our ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PHYB_ARATH PHYB_ARATH] Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region. Photoconversion of Pr to Pfr induces an array of morphogenetic responses, whereas reconversion of Pfr to Pr cancels the induction of those responses. Pfr controls the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase, rRNA, etc. It also controls the expression of its own gene(s) in a negative feedback fashion. Involved in the flowering time regulation.<ref>PMID:12468726</ref> <ref>PMID:15707897</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 15: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4our" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Burgie, E Sethe.]]
+[[Category: Arabidopsis thaliana]]
-[[Category: Bussell, A N.]]
+[[Category: Large Structures]]
-[[Category: Dubiel, K.]]
+[[Category: Bussell AN]]
-[[Category: Vierstra, R D.]]
+[[Category: Dubiel K]]
-[[Category: Walker, J M.]]
+[[Category: Sethe Burgie E]]
-[[Category: Cytosol/nucleus]]
+[[Category: Vierstra RD]]
-[[Category: Gaf domain]]
+[[Category: Walker JM]]
-[[Category: Gene regulation]]
-[[Category: Hairpin]]
-[[Category: N-terminal extension]]
-[[Category: Pas domain]]
-[[Category: Photosensor]]
-[[Category: Phy domain]]
-[[Category: Phytochrome interacting factor]]
-[[Category: Phytochromobilin]]
-[[Category: Signal transduction]]
-[[Category: Transcription]]

4our

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Current revision

Crystal structure of Arabidopsis thaliana phytochrome B photosensory module

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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