1ztu

From Proteopedia

(Difference between revisions)

Revision as of 08:13, 15 May 2024

Structure of the chromophore binding domain of bacterial phytochrome

Structural highlights

1ztu is a 1 chain structure with sequence from Deinococcus radiodurans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	,
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.

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

Phytochromes are red/far-red light photoreceptors that direct photosensory responses across the bacterial, fungal and plant kingdoms. These include photosynthetic potential and pigmentation in bacteria as well as chloroplast development and photomorphogenesis in plants. Phytochromes consist of an amino-terminal region that covalently binds a single bilin chromophore, followed by a carboxy-terminal dimerization domain that often transmits the light signal through a histidine kinase relay. Here we describe the three-dimensional structure of the chromophore-binding domain of Deinococcus radiodurans phytochrome assembled with its chromophore biliverdin in the Pr ground state. Our model, refined to 2.5 A resolution, reaffirms Cys 24 as the chromophore attachment site, locates key amino acids that form a solvent-shielded bilin-binding pocket, and reveals an unusually formed deep trefoil knot that stabilizes this region. The structure provides the first three-dimensional glimpse into the photochromic behaviour of these photoreceptors and helps to explain the evolution of higher plant phytochromes from prokaryotic precursors.

A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome.,Wagner JR, Brunzelle JS, Forest KT, Vierstra RD Nature. 2005 Nov 17;438(7066):325-31. PMID:16292304^[1]

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

References

↑ Wagner JR, Brunzelle JS, Forest KT, Vierstra RD. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature. 2005 Nov 17;438(7066):325-31. PMID:16292304 doi:http://dx.doi.org/10.1038/nature04118

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/1ztu"

@@ Line 3: / Line 3: @@
 <StructureSection load='1ztu' size='340' side='right'caption='[[1ztu]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ztu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZTU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZTU FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</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]] 2.5&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BLA:BILIVERDINE+IX+ALPHA'>BLA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bphP ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1299 "Micrococcus radiodurans" Raj et al. 1960])</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=1ztu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ztu OCA], [https://pdbe.org/1ztu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ztu RCSB], [https://www.ebi.ac.uk/pdbsum/1ztu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ztu ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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.
+[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.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Micrococcus radiodurans raj et al. 1960]]
+[[Category: Deinococcus radiodurans]]
 [[Category: Large Structures]]
-[[Category: Brunzelle, J S]]
+[[Category: Brunzelle JS]]
-[[Category: Forest, K T]]
+[[Category: Forest KT]]
-[[Category: Vierstra, R D]]
+[[Category: Vierstra RD]]
-[[Category: Wagner, J R]]
+[[Category: Wagner JR]]
-[[Category: Bacteriophytochrome]]
-[[Category: Biliverdin ix]]
-[[Category: Chromophore]]
-[[Category: Gaf]]
-[[Category: Knot]]
-[[Category: Pa]]
-[[Category: Phytochrome]]
-[[Category: Transferase]]

1ztu

From Proteopedia

Revision as of 08:13, 15 May 2024

Structure of the chromophore binding domain of bacterial phytochrome

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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