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5nfx

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Revision as of 06:10, 6 June 2018

Deinococcus radiodurans BphP PAS-GAF Y263F mutant

Structural highlights

5nfx is a 1 chain structure with sequence from Deira. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	bphP, DR_A0050 (DEIRA)
Activity:	Histidine kinase, with EC number 2.7.13.3
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

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/5nfx"

@@ Line 3: / Line 3: @@
 <StructureSection load='5nfx' size='340' side='right' caption='[[5nfx]], [[Resolution|resolution]] 1.34&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5nfx]] is a 1 chain structure. 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 [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>
 </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>
+<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='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'>[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>
@@ Line 23: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Deira]]
 [[Category: Histidine kinase]]
 [[Category: Ihalainen, J A]]

5nfx

From Proteopedia

Revision as of 06:10, 6 June 2018

Deinococcus radiodurans BphP PAS-GAF Y263F mutant

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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