1zgo

From Proteopedia

(Difference between revisions)

Current revision

High Resolution Crystal Structure of the Discosoma Red Fluorescent Protein (DsRed)

Structural highlights

1zgo is a 4 chain structure with sequence from Discosoma sp.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.4Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RFP_DISSP Thought to play a role in photoprotection of the coral's resident symbiont microalgae's photosystems from photoinhibition caused by high light levels found near the surface of coral reefs. In deeper water, the fluorescence may be to convert blue light into longer wavelengths more suitable for use in photosynthesis by the microalgal symbionts.^[1]

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

The mature self-synthesizing p-hydroxybenzylideneimidazolinone-like fluorophores of Discosoma red fluorescent protein (DsRed) and Aequorea victoria green fluorescent protein (GFP) are extensively studied as powerful biological markers. Yet, the spontaneous formation of these fluorophores by cyclization, oxidation, and dehydration reactions of tripeptides within their protein environment remains incompletely understood. The mature DsRed fluorophore (Gln 66, Tyr 67, and Gly 68) differs from the GFP fluorophore by an acylimine that results in Gln 66 Calpha planar geometry and by a Phe 65-Gln 66 cis peptide bond. DsRed green-to-red maturation includes a green-fluorescing immature chromophore and requires a chromophore peptide bond trans-cis isomerization that is slow and incomplete. To clarify the unique structural chemistry for the individual immature "green" and mature "red" chromophores of DsRed, we report here the determination and analysis of crystal structures for the wild-type protein (1.4 A resolution), the entirely green DsRed K70M mutant protein (1.9 A resolution), and the DsRed designed mutant Q66M (1.9 A resolution), which shows increased red chromophore relative to the wild-type DsRed. Whereas the mature, red-fluorescing chromophore has the expected cis peptide bond and a sp(2)-hybridized Gln 66 Calpha with planar geometry, the crystal structure of the immature green-fluorescing chromophore of DsRed, presented here for the first time, reveals a trans peptide bond and a sp(3)-hybridized Gln 66 Calpha with tetrahedral geometry. These results characterize a GFP-like immature green DsRed chromophore structure, reveal distinct mature and immature chromophore environments, and furthermore provide evidence for the coupling of acylimine formation with trans-cis isomerization.

Crystallographic structures of Discosoma red fluorescent protein with immature and mature chromophores: linking peptide bond trans-cis isomerization and acylimine formation in chromophore maturation.,Tubbs JL, Tainer JA, Getzoff ED Biochemistry. 2005 Jul 26;44(29):9833-40. PMID:16026155^[2]

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

References

↑ Matz MV, Fradkov AF, Labas YA, Savitsky AP, Zaraisky AG, Markelov ML, Lukyanov SA. Fluorescent proteins from nonbioluminescent Anthozoa species. Nat Biotechnol. 1999 Oct;17(10):969-73. PMID:10504696 doi:http://dx.doi.org/10.1038/13657
↑ Tubbs JL, Tainer JA, Getzoff ED. Crystallographic structures of Discosoma red fluorescent protein with immature and mature chromophores: linking peptide bond trans-cis isomerization and acylimine formation in chromophore maturation. Biochemistry. 2005 Jul 26;44(29):9833-40. PMID:16026155 doi:10.1021/bi0472907

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1zgo"

Categories: Discosoma sp | Large Structures | Getzoff ED | Tainer JA | Tubbs JL

@@ Line 1: / Line 1: @@
 ==High Resolution Crystal Structure of the Discosoma Red Fluorescent Protein (DsRed)==
-<StructureSection load='1zgo' size='340' side='right' caption='[[1zgo]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+<StructureSection load='1zgo' size='340' side='right'caption='[[1zgo]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1zgo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Discosoma_sp. Discosoma sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZGO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZGO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1zgo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Discosoma_sp. Discosoma sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZGO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZGO FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRQ:[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC+ACID'>CRQ</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]] 1.4&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zgp|1zgp]], [[1zgq|1zgq]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRQ:[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC+ACID'>CRQ</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zgo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zgo RCSB], [http://www.ebi.ac.uk/pdbsum/1zgo PDBsum]</span></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=1zgo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zgo OCA], [https://pdbe.org/1zgo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zgo RCSB], [https://www.ebi.ac.uk/pdbsum/1zgo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zgo ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RFP_DISSP RFP_DISSP] Thought to play a role in photoprotection of the coral's resident symbiont microalgae's photosystems from photoinhibition caused by high light levels found near the surface of coral reefs. In deeper water, the fluorescence may be to convert blue light into longer wavelengths more suitable for use in photosynthesis by the microalgal symbionts.<ref>PMID:10504696</ref>
 == 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/zg/1zgo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zg/1zgo_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1zgo ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1zgo" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Green Fluorescent Protein|Green Fluorescent Protein]]
+*[[Green Fluorescent Protein 3D structures|Green Fluorescent Protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Discosoma sp.]]
+[[Category: Discosoma sp]]
-[[Category: Getzoff, E D.]]
+[[Category: Large Structures]]
-[[Category: Tainer, J A.]]
+[[Category: Getzoff ED]]
-[[Category: Tubbs, J L.]]
+[[Category: Tainer JA]]
-[[Category: Beta barrel]]
+[[Category: Tubbs JL]]
-[[Category: Beta can]]
-[[Category: Chromophore]]
-[[Category: Coral]]
-[[Category: Drfp583]]
-[[Category: Dsred]]
-[[Category: Fluorescent protein]]
-[[Category: Gfp]]
-[[Category: Luminescent protein]]
-[[Category: Red]]
-[[Category: Rfp]]

1zgo

From Proteopedia

Current revision

High Resolution Crystal Structure of the Discosoma Red Fluorescent Protein (DsRed)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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