This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2vea

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

The complete sensory module of the cyanobacterial phytochrome Cph1 in the Pr-state.

Structural highlights

2vea is a 1 chain structure with sequence from Aphanocapsa sp. (strain n-1). 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

[PHY1_SYNY3] Regulatory 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. Forms a two-component system with the rcp1 response regulator.

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 photochromic biliprotein photoreceptors, which in plants regulate seed germination, stem extension, flowering time, and many other light effects. However, the structure/functional basis of the phytochrome photoswitch is still unclear. Here, we report the ground state structure of the complete sensory module of Cph1 phytochrome from the cyanobacterium Synechocystis 6803. Although the phycocyanobilin (PCB) chromophore is attached to Cys-259 as expected, paralleling the situation in plant phytochromes but contrasting to that in bacteriophytochromes, the ZZZssa conformation does not correspond to that expected from Raman spectroscopy. We show that the PHY domain, previously considered unique to phytochromes, is structurally a member of the GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) family. Indeed, the tandem-GAF dumbbell revealed for phytochrome sensory modules is remarkably similar to the regulatory domains of cyclic nucleotide (cNMP) phosphodiesterases and adenylyl cyclases. A unique feature of the phytochrome structure is a long, tongue-like protrusion from the PHY domain that seals the chromophore pocket and stabilizes the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue. The structure that we present provides a framework for light-driven signal transmission in phytochromes.

The structure of a complete phytochrome sensory module in the Pr ground state.,Essen LO, Mailliet J, Hughes J Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14709-14. Epub 2008 Sep 17. PMID:18799745^[1]

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

References

↑ Essen LO, Mailliet J, Hughes J. The structure of a complete phytochrome sensory module in the Pr ground state. Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14709-14. Epub 2008 Sep 17. PMID:18799745

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/2vea"

@@ Line 1: / Line 1: @@
 ==The complete sensory module of the cyanobacterial phytochrome Cph1 in the Pr-state.==
-<StructureSection load='2vea' size='340' side='right' caption='[[2vea]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
+<StructureSection load='2vea' size='340' side='right'caption='[[2vea]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vea]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aphanocapsa_sp._(strain_n-1) Aphanocapsa sp. (strain n-1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VEA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vea]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aphanocapsa_sp._(strain_n-1) Aphanocapsa sp. (strain n-1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VEA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VEA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene></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=2vea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vea OCA], [http://pdbe.org/2vea PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vea RCSB], [http://www.ebi.ac.uk/pdbsum/2vea 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=2vea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vea OCA], [https://pdbe.org/2vea PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vea RCSB], [https://www.ebi.ac.uk/pdbsum/2vea PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vea ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PHY1_SYNY3 PHY1_SYNY3]] Regulatory 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. Forms a two-component system with the rcp1 response regulator.
+[[https://www.uniprot.org/uniprot/PHY1_SYNY3 PHY1_SYNY3]] Regulatory 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. Forms a two-component system with the rcp1 response regulator.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ve/2vea_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ve/2vea_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Essen, L O]]
 [[Category: Hughes, J]]

2vea

From Proteopedia

Current revision

The complete sensory module of the cyanobacterial phytochrome Cph1 in the Pr-state.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox