4nbm

From Proteopedia

(Difference between revisions)

Revision as of 08:20, 11 January 2023

Crystal structure of UVB photoreceptor UVR8 and light-induced structural changes at 180K

Structural highlights

4nbm is a 4 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

UVR8_ARATH UV-B specific signaling component that acts as UV-B photoreceptor and plays a key role in establishing UV-protective responses in plants. Upon UV-B irradiation, UVR8 undergoes an immediate switch from homodimer to monomer, accumulates in the nucleus, interacts with the photomorphogenic repressor COP1 and regulates the expression of the transcription factor HY5 by associating with chromatin (through histone H2B binding) in the HY5 promoter region. UVR8 is involved in controlling aspects of leaf growth and morphogenesis in response to UV-B, is required for normal progression of endocycle and has a regulatory role in stomatal differentiation. Is required for plant circadian clock response to photomorphogenic UV-B light, partly through the transcriptional activation of responsive clock genes. Promotes photosynthetic efficiency at elevated levels of UV-B. Plays a role in mediating the effects of UV-B radiation on pathogen resistance by controlling the expression of the sinapate biosynthetic pathway. The two tryptophans, Trp-285 and Trp-233, serve collectively as the UV-B chromophore.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12]

Publication Abstract from PubMed

Arabidopsis thaliana UVR8 (AtUVR8) is a long-sought-after photoreceptor that undergoes dimer dissociation in response to UV-B light. Crystallographic and mutational studies have identified two crucial tryptophan residues for UV-B responses in AtUVR8. However, the mechanism of UV-B perception and structural events leading up to dimer dissociation remain elusive at the molecular level. We applied dynamic crystallography to capture light-induced structural events in photoactive AtUVR8 crystals. Here we report two intermediate structures at 1.67A resolution. At the epicenter of UV-B signaling, concerted motions associated with Trp285/Trp233 lead to ejection of a water molecule, which weakens an intricate network of hydrogen bonds and salt bridges at the dimer interface. Partial opening of the beta-propeller structure due to thermal relaxation of conformational strains originating in the epicenter further disrupts the dimer interface and leads to dimer dissociation. These dynamic crystallographic observations provide structural insights into the photo-perception and signaling mechanism of UVR8.

Dynamic Crystallography Reveals Early Signalling Events in Ultraviolet Photoreceptor UVR8.,Zeng X, Ren Z, Wu Q, Fan J, Peng PP, Tang K, Zhang R, Zhao KH, Yang X Nat Plants. 2015;1. pii: 14006. PMID:26097745^[13]

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

References

↑ Brown BA, Cloix C, Jiang GH, Kaiserli E, Herzyk P, Kliebenstein DJ, Jenkins GI. A UV-B-specific signaling component orchestrates plant UV protection. Proc Natl Acad Sci U S A. 2005 Dec 13;102(50):18225-30. Epub 2005 Dec 5. PMID:16330762 doi:http://dx.doi.org/10.1073/pnas.0507187102
↑ Kaiserli E, Jenkins GI. UV-B promotes rapid nuclear translocation of the Arabidopsis UV-B specific signaling component UVR8 and activates its function in the nucleus. Plant Cell. 2007 Aug;19(8):2662-73. Epub 2007 Aug 24. PMID:17720867 doi:http://dx.doi.org/10.1105/tpc.107.053330
↑ Brown BA, Jenkins GI. UV-B signaling pathways with different fluence-rate response profiles are distinguished in mature Arabidopsis leaf tissue by requirement for UVR8, HY5, and HYH. Plant Physiol. 2008 Feb;146(2):576-88. Epub 2007 Nov 30. PMID:18055587 doi:http://dx.doi.org/10.1104/pp.107.108456
↑ Favory JJ, Stec A, Gruber H, Rizzini L, Oravecz A, Funk M, Albert A, Cloix C, Jenkins GI, Oakeley EJ, Seidlitz HK, Nagy F, Ulm R. Interaction of COP1 and UVR8 regulates UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. EMBO J. 2009 Mar 4;28(5):591-601. doi: 10.1038/emboj.2009.4. Epub 2009 Jan 22. PMID:19165148 doi:http://dx.doi.org/10.1038/emboj.2009.4
↑ Wargent JJ, Gegas VC, Jenkins GI, Doonan JH, Paul ND. UVR8 in Arabidopsis thaliana regulates multiple aspects of cellular differentiation during leaf development in response to ultraviolet B radiation. New Phytol. 2009;183(2):315-26. doi: 10.1111/j.1469-8137.2009.02855.x. Epub 2009 , Apr 27. PMID:19402876 doi:http://dx.doi.org/10.1111/j.1469-8137.2009.02855.x
↑ Gruber H, Heijde M, Heller W, Albert A, Seidlitz HK, Ulm R. Negative feedback regulation of UV-B-induced photomorphogenesis and stress acclimation in Arabidopsis. Proc Natl Acad Sci U S A. 2010 Nov 16;107(46):20132-7. doi:, 10.1073/pnas.0914532107. Epub 2010 Nov 1. PMID:21041653 doi:http://dx.doi.org/10.1073/pnas.0914532107
↑ Feher B, Kozma-Bognar L, Kevei E, Hajdu A, Binkert M, Davis SJ, Schafer E, Ulm R, Nagy F. Functional interaction of the circadian clock and UV RESISTANCE LOCUS 8-controlled UV-B signaling pathways in Arabidopsis thaliana. Plant J. 2011 Jul;67(1):37-48. doi: 10.1111/j.1365-313X.2011.04573.x. Epub 2011, Apr 26. PMID:21395889 doi:http://dx.doi.org/10.1111/j.1365-313X.2011.04573.x
↑ Rizzini L, Favory JJ, Cloix C, Faggionato D, O'Hara A, Kaiserli E, Baumeister R, Schafer E, Nagy F, Jenkins GI, Ulm R. Perception of UV-B by the Arabidopsis UVR8 protein. Science. 2011 Apr 1;332(6025):103-6. doi: 10.1126/science.1200660. PMID:21454788 doi:http://dx.doi.org/10.1126/science.1200660
↑ Demkura PV, Ballare CL. UVR8 mediates UV-B-induced Arabidopsis defense responses against Botrytis cinerea by controlling sinapate accumulation. Mol Plant. 2012 May;5(3):642-52. doi: 10.1093/mp/sss025. Epub 2012 Mar 23. PMID:22447155 doi:http://dx.doi.org/10.1093/mp/sss025
↑ Davey MP, Susanti NI, Wargent JJ, Findlay JE, Paul Quick W, Paul ND, Jenkins GI. The UV-B photoreceptor UVR8 promotes photosynthetic efficiency in Arabidopsis thaliana exposed to elevated levels of UV-B. Photosynth Res. 2012 Dec;114(2):121-31. doi: 10.1007/s11120-012-9785-y. Epub 2012, Nov 19. PMID:23161229 doi:http://dx.doi.org/10.1007/s11120-012-9785-y
↑ O'Hara A, Jenkins GI. In vivo function of tryptophans in the Arabidopsis UV-B photoreceptor UVR8. Plant Cell. 2012 Sep;24(9):3755-66. doi: 10.1105/tpc.112.101451. Epub 2012 Sep, 25. PMID:23012433 doi:http://dx.doi.org/10.1105/tpc.112.101451
↑ Cloix C, Kaiserli E, Heilmann M, Baxter KJ, Brown BA, O'Hara A, Smith BO, Christie JM, Jenkins GI. C-terminal region of the UV-B photoreceptor UVR8 initiates signaling through interaction with the COP1 protein. Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16366-70. doi:, 10.1073/pnas.1210898109. Epub 2012 Sep 17. PMID:22988111 doi:http://dx.doi.org/10.1073/pnas.1210898109
↑ Zeng X, Ren Z, Wu Q, Fan J, Peng PP, Tang K, Zhang R, Zhao KH, Yang X. Dynamic Crystallography Reveals Early Signalling Events in Ultraviolet Photoreceptor UVR8. Nat Plants. 2015;1. pii: 14006. PMID:26097745 doi:http://dx.doi.org/10.1038/nplants.2014.6

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/4nbm"

@@ Line 3: / Line 3: @@
 <StructureSection load='4nbm' size='340' side='right'caption='[[4nbm]], [[Resolution|resolution]] 1.61&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4nbm]] is a 4 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=4NBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4NBM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4nbm]] is a 4 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=4NBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4NBM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4naa|4naa]], [[4nc4|4nc4]]</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=4nbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbm OCA], [https://pdbe.org/4nbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4nbm RCSB], [https://www.ebi.ac.uk/pdbsum/4nbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbm ProSAT]</span></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At5g63860, MGI19.7, UVR8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=4nbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4nbm OCA], [http://pdbe.org/4nbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4nbm RCSB], [http://www.ebi.ac.uk/pdbsum/4nbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4nbm ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/UVR8_ARATH UVR8_ARATH]] UV-B specific signaling component that acts as UV-B photoreceptor and plays a key role in establishing UV-protective responses in plants. Upon UV-B irradiation, UVR8 undergoes an immediate switch from homodimer to monomer, accumulates in the nucleus, interacts with the photomorphogenic repressor COP1 and regulates the expression of the transcription factor HY5 by associating with chromatin (through histone H2B binding) in the HY5 promoter region. UVR8 is involved in controlling aspects of leaf growth and morphogenesis in response to UV-B, is required for normal progression of endocycle and has a regulatory role in stomatal differentiation. Is required for plant circadian clock response to photomorphogenic UV-B light, partly through the transcriptional activation of responsive clock genes. Promotes photosynthetic efficiency at elevated levels of UV-B. Plays a role in mediating the effects of UV-B radiation on pathogen resistance by controlling the expression of the sinapate biosynthetic pathway. The two tryptophans, Trp-285 and Trp-233, serve collectively as the UV-B chromophore.<ref>PMID:16330762</ref> <ref>PMID:17720867</ref> <ref>PMID:18055587</ref> <ref>PMID:19165148</ref> <ref>PMID:19402876</ref> <ref>PMID:21041653</ref> <ref>PMID:21395889</ref> <ref>PMID:21454788</ref> <ref>PMID:22447155</ref> <ref>PMID:23161229</ref> <ref>PMID:23012433</ref> <ref>PMID:22988111</ref>
+[https://www.uniprot.org/uniprot/UVR8_ARATH UVR8_ARATH] UV-B specific signaling component that acts as UV-B photoreceptor and plays a key role in establishing UV-protective responses in plants. Upon UV-B irradiation, UVR8 undergoes an immediate switch from homodimer to monomer, accumulates in the nucleus, interacts with the photomorphogenic repressor COP1 and regulates the expression of the transcription factor HY5 by associating with chromatin (through histone H2B binding) in the HY5 promoter region. UVR8 is involved in controlling aspects of leaf growth and morphogenesis in response to UV-B, is required for normal progression of endocycle and has a regulatory role in stomatal differentiation. Is required for plant circadian clock response to photomorphogenic UV-B light, partly through the transcriptional activation of responsive clock genes. Promotes photosynthetic efficiency at elevated levels of UV-B. Plays a role in mediating the effects of UV-B radiation on pathogen resistance by controlling the expression of the sinapate biosynthetic pathway. The two tryptophans, Trp-285 and Trp-233, serve collectively as the UV-B chromophore.<ref>PMID:16330762</ref> <ref>PMID:17720867</ref> <ref>PMID:18055587</ref> <ref>PMID:19165148</ref> <ref>PMID:19402876</ref> <ref>PMID:21041653</ref> <ref>PMID:21395889</ref> <ref>PMID:21454788</ref> <ref>PMID:22447155</ref> <ref>PMID:23161229</ref> <ref>PMID:23012433</ref> <ref>PMID:22988111</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Arath]]
+[[Category: Arabidopsis thaliana]]
 [[Category: Large Structures]]
-[[Category: Ren, Z]]
+[[Category: Ren Z]]
-[[Category: Yang, X]]
+[[Category: Yang X]]
-[[Category: Zeng, X]]
+[[Category: Zeng X]]
-[[Category: Zhao, K H]]
+[[Category: Zhao K-H]]
-[[Category: 7-blade beta-propeller]]
-[[Category: Gene regulation]]

4nbm

From Proteopedia

Revision as of 08:20, 11 January 2023

Crystal structure of UVB photoreceptor UVR8 and light-induced structural changes at 180K

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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