View source for 2d01


==Wild Type Photoactive Yellow Protein, P65 Form==
<StructureSection load='2d01' size='340' side='right'caption='[[2d01]], [[Resolution|resolution]] 1.34&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2d01]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. The March 2015 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Phototropin''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2015_3 10.2210/rcsb_pdb/mom_2015_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D01 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D01 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.34&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</scene></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=2d01 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d01 OCA], [https://pdbe.org/2d01 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d01 RCSB], [https://www.ebi.ac.uk/pdbsum/2d01 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d01 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
== 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/d0/2d01_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2d01 ConSurf].
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== Publication Abstract from PubMed ==
Mutating arginine 52 to glutamine (R52Q) in photoactive yellow protein (PYP) increases the pK(a) of the chromophore by 1 pH unit. The structure of the R52Q PYP mutant was determined by X-ray crystallography and was compared to the structure of wild-type PYP to assess the role of R52 in pK(a) regulation. The essential differences between R52Q and the wild type were confined to the loop region containing the 52nd residue. While the hydrogen bonds involving the chromophore were unchanged by the mutation, removing the guanidino group generated a cavity near the chromophore; this cavity is occupied by two water molecules. In the wild type, R52 forms hydrogen bonds with T50 and Y98; these hydrogen bonds are lost in R52Q. Q52 is linked to Y98 by hydrogen bonding through the two water molecules. R52 acts as a lid on the chromophore binding pocket and controls the accessibility of the exterior solvent and the pK(a) of the chromophore. R52 is found to flip out during the formation of PYP(M). The result of this movement is quite similar to the altered structure of R52Q. Thus, we propose that conformational changes at R52 are partly responsible for pK(a) regulation during the photocycle.

The crystal structure of the R52Q mutant demonstrates a role for R52 in chromophore pKa regulation in photoactive yellow protein.,Shimizu N, Kamikubo H, Yamazaki Y, Imamoto Y, Kataoka M Biochemistry. 2006 Mar 21;45(11):3542-7. PMID:16533035<ref>PMID:16533035</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2d01" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Halorhodospira halophila]]
[[Category: Large Structures]]
[[Category: Phototropin]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Imamoto Y]]
[[Category: Kamikubo H]]
[[Category: Kataoka M]]
[[Category: Shimizu N]]
[[Category: Yamazaki Y]]