2k2n: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:2k2n.png|left|200px]]


<!--
==Solution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state==
The line below this paragraph, containing "STRUCTURE_2k2n", creates the "Structure Box" on the page.
<StructureSection load='2k2n' size='340' side='right'caption='[[2k2n]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2k2n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synechococcus_sp._RCC307 Synechococcus sp. RCC307]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K2N FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</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>
{{STRUCTURE_2k2n|  PDB=2k2n  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2k2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k2n OCA], [https://pdbe.org/2k2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k2n RCSB], [https://www.ebi.ac.uk/pdbsum/2k2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k2n ProSAT], [https://www.topsan.org/Proteins/CESG/2k2n TOPSAN]</span></td></tr>
</table>
== 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/k2/2k2n_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2k2n ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The unique photochromic absorption behavior of phytochromes (Phys) depends on numerous reversible interactions between the bilin chromophore and the associated polypeptide. To help define these dynamic interactions, we determined by NMR spectroscopy the first solution structure of the chromophore-binding cGMP phosphodiesterase/adenylcyclase/FhlA (GAF) domain from a cyanobacterial Phy assembled with phycocyanobilin (PCB). The three-dimensional NMR structure of Synechococcus OS-B' cyanobacterial Phy 1 in the red-light-absorbing state of Phy (Pr) revealed that PCB is bound to Cys138 of the GAF domain via the A-ring ethylidene side chain and is buried within the GAF domain in a ZZZsyn,syn,anti configuration. The D ring of the chromophore sits within a hydrophobic pocket and is tilted by approximately 80 degrees relative to the B/C rings by contacts with Lys52 and His169. The solution structure revealed remarkable flexibility for PCB and several adjacent amino acids, indicating that the Pr chromophore has more freedom in the binding pocket than anticipated. The propionic acid side chains of rings B and C and Arg101 and Arg133 nearby are especially mobile and can assume several distinct and energetically favorable conformations. Mutagenic studies on these arginines, which are conserved within the Phy superfamily, revealed that they have opposing roles, with Arg101 and Arg133 helping stabilize and destabilize the far-red-light-absorbing state of Phy (Pfr), respectively. Given the fact that the Synechococcus OS-B' GAF domain can, by itself, complete the Pr --&gt; Pfr photocycle, it should now be possible to determine the solution structure of the Pfr chromophore and surrounding pocket using this Pr structure as a framework.


===Solution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state===
Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state.,Cornilescu G, Ulijasz AT, Cornilescu CC, Markley JL, Vierstra RD J Mol Biol. 2008 Nov 7;383(2):403-13. Epub 2008 Aug 22. PMID:18762196<ref>PMID:18762196</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<!--
</div>
The line below this paragraph, {{ABSTRACT_PUBMED_18762196}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2k2n" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 18762196 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18762196}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2K2N is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Synechococcus_sp. Synechococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K2N OCA].
[[Category: Synechococcus sp. RCC307]]
 
[[Category: Cornilescu CC]]
==Reference==
[[Category: Cornilescu G]]
Solution Structure of a Cyanobacterial Phytochrome GAF Domain in the Red-Light-Absorbing Ground State., Cornilescu G, Ulijasz AT, Cornilescu CC, Markley JL, Vierstra RD, J Mol Biol. 2008 Aug 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18762196 18762196]
[[Category: Markley JL]]
[[Category: Histidine kinase]]
[[Category: Ulijasz AT]]
[[Category: Single protein]]
[[Category: Vierstra RD]]
[[Category: Synechococcus sp.]]
[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
[[Category: Bacteriophytochrome]]
[[Category: Cyanobacterial phytochrome]]
[[Category: Gaf domain]]
[[Category: Kinase]]
[[Category: Pcb]]
[[Category: Phosphoprotein]]
[[Category: Phycocyanobilin]]
[[Category: Phytochrome]]
[[Category: Transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 24 20:31:54 2008''

Latest revision as of 09:09, 27 November 2024

Solution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground stateSolution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state

Structural highlights

2k2n is a 1 chain structure with sequence from Synechococcus sp. RCC307. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR, 20 models
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

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

The unique photochromic absorption behavior of phytochromes (Phys) depends on numerous reversible interactions between the bilin chromophore and the associated polypeptide. To help define these dynamic interactions, we determined by NMR spectroscopy the first solution structure of the chromophore-binding cGMP phosphodiesterase/adenylcyclase/FhlA (GAF) domain from a cyanobacterial Phy assembled with phycocyanobilin (PCB). The three-dimensional NMR structure of Synechococcus OS-B' cyanobacterial Phy 1 in the red-light-absorbing state of Phy (Pr) revealed that PCB is bound to Cys138 of the GAF domain via the A-ring ethylidene side chain and is buried within the GAF domain in a ZZZsyn,syn,anti configuration. The D ring of the chromophore sits within a hydrophobic pocket and is tilted by approximately 80 degrees relative to the B/C rings by contacts with Lys52 and His169. The solution structure revealed remarkable flexibility for PCB and several adjacent amino acids, indicating that the Pr chromophore has more freedom in the binding pocket than anticipated. The propionic acid side chains of rings B and C and Arg101 and Arg133 nearby are especially mobile and can assume several distinct and energetically favorable conformations. Mutagenic studies on these arginines, which are conserved within the Phy superfamily, revealed that they have opposing roles, with Arg101 and Arg133 helping stabilize and destabilize the far-red-light-absorbing state of Phy (Pfr), respectively. Given the fact that the Synechococcus OS-B' GAF domain can, by itself, complete the Pr --> Pfr photocycle, it should now be possible to determine the solution structure of the Pfr chromophore and surrounding pocket using this Pr structure as a framework.

Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state.,Cornilescu G, Ulijasz AT, Cornilescu CC, Markley JL, Vierstra RD J Mol Biol. 2008 Nov 7;383(2):403-13. Epub 2008 Aug 22. PMID:18762196[1]

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

References

  1. ↑ Cornilescu G, Ulijasz AT, Cornilescu CC, Markley JL, Vierstra RD. Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state. J Mol Biol. 2008 Nov 7;383(2):403-13. Epub 2008 Aug 22. PMID:18762196 doi:10.1016/j.jmb.2008.08.034
Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=2k2n&oldid=4205339"