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| | ==Crystal structure of red fluorescent gene-engineered variant with improved folding - lanRFP_delS83 (Branchiostoma lanceolatum)== | | ==Crystal structure of red fluorescent gene-engineered variant with improved folding - lanRFP_delS83 (Branchiostoma lanceolatum)== |
| - | <StructureSection load='4jge' size='340' side='right' caption='[[4jge]], [[Resolution|resolution]] 1.94Å' scene=''> | + | <StructureSection load='4jge' size='340' side='right'caption='[[4jge]], [[Resolution|resolution]] 1.94Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4jge]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Branchiostoma_lanceolatum Branchiostoma lanceolatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JGE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JGE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4jge]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Branchiostoma_lanceolatum Branchiostoma lanceolatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JGE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JGE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.94Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CR2:{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CR2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4jf9|4jf9]], [[4hvf|4hvf]], [[2g3o|2g3o]], [[2dd7|2dd7]], [[4jeo|4jeo]]</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=4jge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jge OCA], [https://pdbe.org/4jge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jge RCSB], [https://www.ebi.ac.uk/pdbsum/4jge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jge ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">blFP-R5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7740 Branchiostoma lanceolatum])</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=4jge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jge OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jge RCSB], [http://www.ebi.ac.uk/pdbsum/4jge PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/B1PND0_BRALA B1PND0_BRALA] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4jge" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Branchiostoma lanceolatum]] | | [[Category: Branchiostoma lanceolatum]] |
| - | [[Category: Pletnev, S V]] | + | [[Category: Large Structures]] |
| - | [[Category: Pletnev, V Z]] | + | [[Category: Pletnev SV]] |
| - | [[Category: Pletneva, N V]] | + | [[Category: Pletnev VZ]] |
| - | [[Category: Beta-barrel]] | + | [[Category: Pletneva NV]] |
| - | [[Category: Cephalochordate]]
| + | |
| - | [[Category: Fluorescent protein]]
| + | |
| - | [[Category: Fluoresent protein]]
| + | |
| - | [[Category: Gly-tyr-gly chromophore]]
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| - | [[Category: Lanrfp]]
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| Structural highlights
Function
B1PND0_BRALA
Publication Abstract from PubMed
A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the `core' structure, which can be extended in red-shifted proteins owing to modifications of the protein backbone at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (lambdaex/lambdaem = 502/511 nm) and red laRFP (lambdaex/lambdaem approximately 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-DeltaS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only approximately 20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 C(beta) atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift ( approximately 70 nm) of laRFP was verified by extensive structure-based site-directed mutagenesis.
Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine.,Pletnev VZ, Pletneva NV, Lukyanov KA, Souslova EA, Fradkov AF, Chudakov DM, Chepurnykh T, Yampolsky IV, Wlodawer A, Dauter Z, Pletnev S Acta Crystallogr D Biol Crystallogr. 2013 Sep 1;69(Pt 9):1850-60. doi:, 10.1107/S0907444913015424. Epub 2013 Aug 17. PMID:23999308[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Pletnev VZ, Pletneva NV, Lukyanov KA, Souslova EA, Fradkov AF, Chudakov DM, Chepurnykh T, Yampolsky IV, Wlodawer A, Dauter Z, Pletnev S. Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine. Acta Crystallogr D Biol Crystallogr. 2013 Sep 1;69(Pt 9):1850-60. doi:, 10.1107/S0907444913015424. Epub 2013 Aug 17. PMID:23999308 doi:10.1107/S0907444913015424
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