3phy: Difference between revisions
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== | ==PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED), SOLUTION STRUCTURE, NMR, 26 STRUCTURES== | ||
[[3phy]] is a 1 chain structure with sequence from [ | <StructureSection load='3phy' size='340' side='right'caption='[[3phy]], [[NMR_Ensembles_of_Models | 26 NMR models]]' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3phy]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PHY FirstGlance]. <br> | |||
</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=3phy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3phy OCA], [https://pdbe.org/3phy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3phy RCSB], [https://www.ebi.ac.uk/pdbsum/3phy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3phy 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/ph/3phy_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=3phy ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The solution structure of photoactive yellow protein (PYP), a photosensory protein from Ectothiorhodospira halophila, has been determined by multidimensional NMR spectroscopy. The structure consists of an open, twisted, 6-stranded, antiparallel beta-sheet, which is flanked by four alpha-helices on both sides. The final set of 26 selected structures is well-defined for the regions spanning residues Phe6-Ala16, Asp24-Ala112, and Tyr118-Val125 and displays a root-mean-square deviation, versus the average, of 0.45 A for the backbone and 0.88 A for all heavy atoms. Comparison of the solution structure with an earlier published 1.4 A crystal structure (Borgstahl, G. E. O., Williams, D. R., and Getzoff, E. D. (1995) Biochemistry 34, 6278-6287) reveals a similarity with a root-mean-square deviation of 1.77 A for the backbone for the well-defined regions. The most distinct difference in the backbone with the crystal structure is found near the N-terminus, for residues Asp19-Leu23, which corresponds to an alpha-helix in the crystal structure and to one of the poorest defined regions in the solution structure. To characterize the dynamic behavior of PYP in solution, we undertook a 15N relaxation study and measurements of hydrogen/deuterium exchange. Determination of order parameters through the model-free Lipari-Szabo approach enabled the identification of several regions of enhanced dynamics. The comparison of atomic displacements in the backbone traces of the ensemble structures, with mobility measurements from NMR, show that the poorly defined regions feature fast internal motions in the nanosecond to picosecond time scale. | |||
Solution structure and backbone dynamics of the photoactive yellow protein.,Dux P, Rubinstenn G, Vuister GW, Boelens R, Mulder FA, Hard K, Hoff WD, Kroon AR, Crielaard W, Hellingwerf KJ, Kaptein R Biochemistry. 1998 Sep 15;37(37):12689-99. PMID:9737845<ref>PMID:9737845</ref> | |||
<ref | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3phy" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Halorhodospira halophila]] | [[Category: Halorhodospira halophila]] | ||
[[Category: Boelens, R | [[Category: Large Structures]] | ||
[[Category: Crielaard, W | [[Category: Boelens, R]] | ||
[[Category: Dux, P | [[Category: Crielaard, W]] | ||
[[Category: Hard, K | [[Category: Dux, P]] | ||
[[Category: Hellingwerf, K J | [[Category: Hard, K]] | ||
[[Category: Hoff, W D | [[Category: Hellingwerf, K J]] | ||
[[Category: Kaptein, R | [[Category: Hoff, W D]] | ||
[[Category: Kroon, A | [[Category: Kaptein, R]] | ||
[[Category: Mulder, F A.A | [[Category: Kroon, A]] | ||
[[Category: Rubinstenn, G | [[Category: Mulder, F A.A]] | ||
[[Category: Vuister, G W | [[Category: Rubinstenn, G]] | ||
[[Category: Vuister, G W]] | |||
[[Category: Light sensor for negative phototaxis]] | [[Category: Light sensor for negative phototaxis]] | ||
[[Category: Photoreceptor]] | [[Category: Photoreceptor]] | ||
Latest revision as of 10:04, 16 March 2022
PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED), SOLUTION STRUCTURE, NMR, 26 STRUCTURESPHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED), SOLUTION STRUCTURE, NMR, 26 STRUCTURES
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 PubMedThe solution structure of photoactive yellow protein (PYP), a photosensory protein from Ectothiorhodospira halophila, has been determined by multidimensional NMR spectroscopy. The structure consists of an open, twisted, 6-stranded, antiparallel beta-sheet, which is flanked by four alpha-helices on both sides. The final set of 26 selected structures is well-defined for the regions spanning residues Phe6-Ala16, Asp24-Ala112, and Tyr118-Val125 and displays a root-mean-square deviation, versus the average, of 0.45 A for the backbone and 0.88 A for all heavy atoms. Comparison of the solution structure with an earlier published 1.4 A crystal structure (Borgstahl, G. E. O., Williams, D. R., and Getzoff, E. D. (1995) Biochemistry 34, 6278-6287) reveals a similarity with a root-mean-square deviation of 1.77 A for the backbone for the well-defined regions. The most distinct difference in the backbone with the crystal structure is found near the N-terminus, for residues Asp19-Leu23, which corresponds to an alpha-helix in the crystal structure and to one of the poorest defined regions in the solution structure. To characterize the dynamic behavior of PYP in solution, we undertook a 15N relaxation study and measurements of hydrogen/deuterium exchange. Determination of order parameters through the model-free Lipari-Szabo approach enabled the identification of several regions of enhanced dynamics. The comparison of atomic displacements in the backbone traces of the ensemble structures, with mobility measurements from NMR, show that the poorly defined regions feature fast internal motions in the nanosecond to picosecond time scale. Solution structure and backbone dynamics of the photoactive yellow protein.,Dux P, Rubinstenn G, Vuister GW, Boelens R, Mulder FA, Hard K, Hoff WD, Kroon AR, Crielaard W, Hellingwerf KJ, Kaptein R Biochemistry. 1998 Sep 15;37(37):12689-99. PMID:9737845[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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