3phy: Difference between revisions

Revision as of 20:10, 21 February 2008

PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED), SOLUTION STRUCTURE, NMR, 26 STRUCTURES

OverviewOverview

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.

About this StructureAbout this Structure

3PHY is a Single protein structure of sequence from Halorhodospira halophila with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

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

Page seeded by OCA on Thu Feb 21 19:10:54 2008

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

OCA

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-[[Image:3phy.jpg|left|200px]]<br /><applet load="3phy" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:3phy.jpg|left|200px]]<br /><applet load="3phy" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="3phy" />
 '''PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED), SOLUTION STRUCTURE, NMR, 26 STRUCTURES'''<br />
 ==Overview==
-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.
+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.
 ==About this Structure==
-PHY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila] with HC4 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=3PHY OCA].
+PHY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila] with <scene name='pdbligand=HC4:'>HC4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PHY OCA].
 ==Reference==
@@ Line 17: / Line 17: @@
 [[Category: Dux, P.]]
 [[Category: Hard, K.]]
-[[Category: Hellingwerf, K.J.]]
+[[Category: Hellingwerf, K J.]]
-[[Category: Hoff, W.D.]]
+[[Category: Hoff, W D.]]
 [[Category: Kaptein, R.]]
 [[Category: Kroon, A.]]
-[[Category: Mulder, F.A.A.]]
+[[Category: Mulder, F A.A.]]
 [[Category: Rubinstenn, G.]]
-[[Category: Vuister, G.W.]]
+[[Category: Vuister, G W.]]
 [[Category: HC4]]
 [[Category: light sensor for negative phototaxis]]
 [[Category: photoreceptor]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:56:06 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:10:54 2008''