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| | ==Deinococcus radiodurans BphP PAS-GAF Y263F mutant== | | ==Deinococcus radiodurans BphP PAS-GAF Y263F mutant== |
| - | <StructureSection load='5nfx' size='340' side='right' caption='[[5nfx]], [[Resolution|resolution]] 1.34Å' scene=''> | + | <StructureSection load='5nfx' size='340' side='right'caption='[[5nfx]], [[Resolution|resolution]] 1.34Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5nfx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Deira Deira]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NFX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NFX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5nfx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NFX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NFX FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 1.34Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bphP, DR_A0050 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243230 DEIRA])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=LBV:3-[2-[(Z)-[3-(2-CARBOXYETHYL)-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YLIDENE)METHYL]-4-METHYL-PYRROL-1-IUM-2-YLIDENE]METHYL]-5-[(Z)-[(3E)-3-ETHYLIDENE-4-METHYL-5-OXIDANYLIDENE-PYRROLIDIN-2-YLIDENE]METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>LBV</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histidine_kinase Histidine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.13.3 2.7.13.3] </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=5nfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nfx OCA], [https://pdbe.org/5nfx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nfx RCSB], [https://www.ebi.ac.uk/pdbsum/5nfx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nfx ProSAT]</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=5nfx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nfx OCA], [http://pdbe.org/5nfx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nfx RCSB], [http://www.ebi.ac.uk/pdbsum/5nfx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nfx ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA]] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light. | + | [https://www.uniprot.org/uniprot/BPHY_DEIRA BPHY_DEIRA] Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Deira]] | + | [[Category: Deinococcus radiodurans R1]] |
| - | [[Category: Histidine kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Ihalainen, J A]] | + | [[Category: Ihalainen JA]] |
| - | [[Category: Takala, H]] | + | [[Category: Takala H]] |
| - | [[Category: Westenhoff, S]] | + | [[Category: Westenhoff S]] |
| - | [[Category: Kinase]]
| + | |
| - | [[Category: Photosensor]]
| + | |
| - | [[Category: Phytochrome]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
BPHY_DEIRA Photoreceptor which exists in two forms that are reversibly interconvertible by light: the R form that absorbs maximally in the red region of the spectrum and the FR form that absorbs maximally in the far-red region. Has also a slight blue shift for the far-red maximum. Could also absorb green light. May participate in regulating pigment synthesis like the carotenoid deinoxanthin which could protect the bacterium from intense visible light.
Publication Abstract from PubMed
Phytochromes are photoreceptors in plants, fungi, and various microorganisms and cycle between metastable red light-absorbing (Pr) and far-red light-absorbing (Pfr) states. Their light responses are thought to follow a conserved structural mechanism that is triggered by isomerization of the chromophore. Downstream structural changes involve refolding of the so-called tongue extension of the phytochrome-specific GAF-related (PHY) domain of the photoreceptor. The tongue is connected to the chromophore by conserved DIP and PRxSF motifs and a conserved tyrosine, but the role of these residues in signal transduction is not clear. Here, we examine the tongue interactions and their interplay with the chromophore by substituting the conserved tyrosine (Tyr-263) in the phytochrome from the extremophile bacterium Deinococcus radiodurans with phenylalanine. Using optical and FTIR spectroscopy, X-ray solution scattering, and crystallography of chromophore-binding domain (CBD) and CBD-PHY fragments, we show that the absence of the Tyr-263 hydroxyl destabilizes the beta-sheet conformation of the tongue. This allowed the phytochrome to adopt an alpha-helical tongue conformation regardless of the chromophore state, hence distorting the activity state of the protein. Our crystal structures further revealed that water interactions are missing in the Y263F mutant, correlating with a decrease of the photoconversion yield and underpinning the functional role of Tyr-263 in phytochrome conformational changes. We propose a model in which isomerization of the chromophore, refolding of the tongue, and globular conformational changes are represented as weakly coupled equilibria. The results also suggest that the phytochromes have several redundant signaling routes.
On the (un)coupling of the chromophore, tongue interactions and overall conformation in a bacterial phytochrome.,Takala H, Lehtivuori H, Berntsson O, Hughes A, Nanekar R, Niebling S, Panman M, Henry L, Menzel A, Westenhoff S, Ihalainen JA J Biol Chem. 2018 Apr 5. pii: RA118.001794. doi: 10.1074/jbc.RA118.001794. PMID:29622676[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Takala H, Lehtivuori H, Berntsson O, Hughes A, Nanekar R, Niebling S, Panman M, Henry L, Menzel A, Westenhoff S, Ihalainen JA. On the (un)coupling of the chromophore, tongue interactions and overall conformation in a bacterial phytochrome. J Biol Chem. 2018 Apr 5. pii: RA118.001794. doi: 10.1074/jbc.RA118.001794. PMID:29622676 doi:http://dx.doi.org/10.1074/jbc.RA118.001794
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