9rn8
From Proteopedia
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(New page: '''Unreleased structure''' The entry 9rn8 is ON HOLD Authors: Sauthof, L., Ebrahim, M., Scheerer, P. Description: Crystal structure of the photosensory core module (PCM) of a cyano-phe...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of the photosensory core module (PCM) of a cyano-phenylalanine mutant oCNF205 of the bathy phytochrome Agp2 from Agrobacterium fabrum in the Pfr state.== | |
| + | <StructureSection load='9rn8' size='340' side='right'caption='[[9rn8]], [[Resolution|resolution]] 1.79Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[9rn8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9RN8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9RN8 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]] 1.79Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9IJ:2-cyano-L-phenylalanine'>9IJ</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EL5:3-[5-[(~{E})-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[(~{Z})-[5-[(~{Z})-[(3~{E},4~{S})-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-2-ylidene]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic+acid'>EL5</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MLZ:N-METHYL-LYSINE'>MLZ</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=9rn8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9rn8 OCA], [https://pdbe.org/9rn8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9rn8 RCSB], [https://www.ebi.ac.uk/pdbsum/9rn8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9rn8 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/A9CI81_AGRFC A9CI81_AGRFC] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | In phytochromes, photoisomerization of the chromophore and subsequent structural relaxations lead to the functionally essential secondary structure transition of the tongue, a phytochrome-specific protein segment. The coupling mechanism between chromophore and protein structural changes is yet not understood, but electric field changes are discussed to play an important role. In this work, electric field changes in the chromophore binding pocket (CBP) are confirmed to propagate over long distances through the protein and alter the electric field in the tongue region. An experimental-theoretical approach to analyze local electric fields using Stark reporters has been further developed. These are nitrile groups introduced site-specifically into the protein via noncanonical amino acids. The functional integrity of the variants is checked by crystallography and various spectroscopies. For the first time, functionally intact variants with substitutions in the tongue are generated. Based on frequency shifts and relative intensities of the nitrile stretching modes, hydrogen-bonding and noncovalent electric field contributions are separated. The field changes originating in the CBP are transduced to the tongue along a pathway via Phe192. Given a proper direction of the net electric field vector in the tongue region, the magnitude of the field may be sufficient to destabilize the tongue structure. | ||
| - | + | Propagation of Photoinduced Electric Field Changes Through Phytochrome and their Impact on Conformational Transitions.,La Greca M, Nguyen AD, Kraskov A, Michael N, Sauthof L, Ebrahim M, Katz S, von Sass J, Hoang OT, Budisa N, Scheerer P, Schlesinger R, Mroginski MA, Hildebrandt P Chemphyschem. 2025 Sep 21:e202500595. doi: 10.1002/cphc.202500595. PMID:40976591<ref>PMID:40976591</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 9rn8" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: Scheerer | + | <references/> |
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Agrobacterium fabrum str. C58]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Ebrahim M]] | ||
| + | [[Category: Sauthof L]] | ||
| + | [[Category: Scheerer P]] | ||
Current revision
Crystal structure of the photosensory core module (PCM) of a cyano-phenylalanine mutant oCNF205 of the bathy phytochrome Agp2 from Agrobacterium fabrum in the Pfr state.
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