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| | ==X-ray Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K== | | ==X-ray Crystal Structure of Photoactive Yellow Protein, Wild type, at 295K== |
| - | <StructureSection load='2zoh' size='340' side='right' caption='[[2zoh]], [[Resolution|resolution]] 1.25Å' scene=''> | + | <StructureSection load='2zoh' size='340' side='right'caption='[[2zoh]], [[Resolution|resolution]] 1.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zoh]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dsm_244 Dsm 244]. The March 2015 RCSB PDB [http://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 [http://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=2ZOH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZOH FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zoh]] 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=2ZOH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZOH FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HC4:4-HYDROXYCINNAMIC+ACID'>HC4</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]] 1.25Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2zoi|2zoi]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pyp ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</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=2zoh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zoh OCA], [https://pdbe.org/2zoh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zoh RCSB], [https://www.ebi.ac.uk/pdbsum/2zoh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zoh ProSAT]</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=2zoh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zoh OCA], [http://pdbe.org/2zoh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zoh RCSB], [http://www.ebi.ac.uk/pdbsum/2zoh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zoh ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PYP_HALHA PYP_HALHA]] Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response. | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Dsm 244]] | + | [[Category: Halorhodospira halophila]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Phototropin]] | | [[Category: Phototropin]] |
| | [[Category: RCSB PDB Molecule of the Month]] | | [[Category: RCSB PDB Molecule of the Month]] |
| - | [[Category: Yamaguchi, S]] | + | [[Category: Yamaguchi S]] |
| - | [[Category: Chromophore]]
| + | |
| - | [[Category: Light sensor]]
| + | |
| - | [[Category: Lov]]
| + | |
| - | [[Category: Pa]]
| + | |
| - | [[Category: Photoreceptor]]
| + | |
| - | [[Category: Photoreceptor protein]]
| + | |
| - | [[Category: Receptor]]
| + | |
| - | [[Category: Sensory transduction]]
| + | |
| - | [[Category: Signaling protein]]
| + | |
| Structural highlights
Function
PYP_HALHA Photoactive blue light protein. Probably functions as a photoreceptor for a negative phototaxis response.
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
Low-barrier hydrogen bonds (LBHBs) have been proposed to play roles in protein functions, including enzymatic catalysis and proton transfer. Transient formation of LBHBs is expected to stabilize specific reaction intermediates. However, based on experimental results and theoretical considerations, arguments against the importance of LBHB in proteins have been raised. The discrepancy is caused by the absence of direct identification of the hydrogen atom position. Here, we show by high-resolution neutron crystallography of photoactive yellow protein (PYP) that a LBHB exists in a protein, even in the ground state. We identified approximately 87% (819/942) of the hydrogen positions in PYP and demonstrated that the hydrogen bond between the chromophore and E46 is a LBHB. This LBHB stabilizes an isolated electric charge buried in the hydrophobic environment of the protein interior. We propose that in the excited state the fast relaxation of the LBHB into a normal hydrogen bond is the trigger for photo-signal propagation to the protein moiety. These results give insights into the novel roles of LBHBs and the mechanism of the formation of LBHBs.
Low-barrier hydrogen bond in photoactive yellow protein.,Yamaguchi S, Kamikubo H, Kurihara K, Kuroki R, Niimura N, Shimizu N, Yamazaki Y, Kataoka M Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):440-4. Epub 2009 Jan 2. PMID:19122140[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yamaguchi S, Kamikubo H, Kurihara K, Kuroki R, Niimura N, Shimizu N, Yamazaki Y, Kataoka M. Low-barrier hydrogen bond in photoactive yellow protein. Proc Natl Acad Sci U S A. 2009 Jan 13;106(2):440-4. Epub 2009 Jan 2. PMID:19122140
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