2qws: Difference between revisions

Latest revision as of 11:42, 30 August 2023

Neutron and X-ray structural studies of short hydrogen bonds in Photoactive Yellow Protein (PYP)

Structural highlights

2qws is a 1 chain structure with sequence from Halorhodospira halophila. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	DOD, HC4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

Photoactive yellow protein (PYP) from Halorhodospira halophila is a soluble 14 kDa blue-light photoreceptor. It absorbs light via its para-coumaric acid chromophore (pCA), which is covalently attached to Cys69 and is believed to be involved in the negative phototactic response of the organism to blue light. The complete structure (including H atoms) of PYP has been determined in D(2)O-soaked crystals through the application of joint X-ray (1.1 A) and neutron (2.5 A) structure refinement in combination with cross-validated maximum-likelihood simulated annealing. The resulting XN structure reveals that the phenolate O atom of pCA accepts deuterons from Glu46 O(epsilon2) and Tyr42 O(eta) in two unusually short hydrogen bonds. This arrangement is stabilized by the donation of a deuteron from Thr50 O(gamma1) to Tyr42 O(eta). However, the deuteron position between pCA and Tyr42 is only partially occupied. Thus, this atom may also interact with Thr50, possibly being disordered or fluctuating between the two bonds.

Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP).,Fisher SZ, Anderson S, Henning R, Moffat K, Langan P, Thiyagarajan P, Schultz AJ Acta Crystallogr D Biol Crystallogr. 2007 Nov;63(Pt 11):1178-84. Epub 2007, Oct 17. PMID:18007033^[1]

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

References

↑ Fisher SZ, Anderson S, Henning R, Moffat K, Langan P, Thiyagarajan P, Schultz AJ. Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP). Acta Crystallogr D Biol Crystallogr. 2007 Nov;63(Pt 11):1178-84. Epub 2007, Oct 17. PMID:18007033 doi:10.1107/S0907444907047646

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OCA

[1] Fisher SZ, Anderson S, Henning R, Moffat K, Langan P, Thiyagarajan P, Schultz AJ. Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP). Acta Crystallogr D Biol Crystallogr. 2007 Nov;63(Pt 11):1178-84. Epub 2007, Oct 17. PMID:18007033 doi:10.1107/S0907444907047646

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='2qws' size='340' side='right'caption='[[2qws]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qws]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dsm_244 Dsm 244]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QWS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QWS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qws]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorhodospira_halophila Halorhodospira halophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QWS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QWS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <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]] 2.5&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pyp ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053 DSM 244])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <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=2qws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qws OCA], [https://pdbe.org/2qws PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qws RCSB], [https://www.ebi.ac.uk/pdbsum/2qws PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qws 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.
+[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]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Dsm 244]]
+[[Category: Halorhodospira halophila]]
 [[Category: Large Structures]]
-[[Category: Fisher, S Z]]
+[[Category: Fisher SZ]]
-[[Category: Langan, P]]
+[[Category: Langan P]]
-[[Category: Chromophore]]
-[[Category: Hydrogen bond]]
-[[Category: Neutron]]
-[[Category: Photocycle]]
-[[Category: Photoreceptor protein]]
-[[Category: Receptor]]
-[[Category: Sensory transduction]]
-[[Category: Signaling protein]]

2qws: Difference between revisions

Latest revision as of 11:42, 30 August 2023

Neutron and X-ray structural studies of short hydrogen bonds in Photoactive Yellow Protein (PYP)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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