1qyf: Difference between revisions

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Revision as of 23:20, 30 March 2008

File:1qyf.jpg

, resolution 1.50Å

Ligands:

, ,

Gene:

GFP (Aequorea victoria)

Related:

1QXT, 1QY3

Resources:

FirstGlance, OCA, PDBsum, RCSB

Coordinates:

save as pdb, mmCIF, xml

Crystal structure of matured green fluorescent protein R96A variant

OverviewOverview

Green fluorescent protein has revolutionized cell labeling and molecular tagging, yet the driving force and mechanism for its spontaneous fluorophore synthesis are not established. Here we discover mutations that substantially slow the rate but not the yield of this posttranslational modification, determine structures of the trapped precyclization intermediate and oxidized postcyclization states, and identify unanticipated features critical to chromophore maturation. The protein architecture contains a dramatic approximately 80 degrees bend in the central helix, which focuses distortions at G67 to promote ring formation from amino acids S65, Y66, and G67. Significantly, these distortions eliminate potential helical hydrogen bonds that would otherwise have to be broken at an energetic cost during peptide cyclization and force the G67 nitrogen and S65 carbonyl oxygen atoms within van der Waals contact in preparation for covalent bond formation. Further, we determine that under aerobic, but not anaerobic, conditions the Gly-Gly-Gly chromophore sequence cyclizes and incorporates an oxygen atom. These results lead directly to a conjugation-trapping mechanism, in which a thermodynamically unfavorable cyclization reaction is coupled to an electronic conjugation trapping step, to drive chromophore maturation. Moreover, we propose primarily electrostatic roles for the R96 and E222 side chains in chromophore formation and suggest that the T62 carbonyl oxygen is the base that initiates the dehydration reaction. Our molecular mechanism provides the basis for understanding and eventually controlling chromophore creation.

About this StructureAbout this Structure

1QYF is a Single protein structure of sequence from Aequorea victoria. Full crystallographic information is available from OCA.

ReferenceReference

Mechanism and energetics of green fluorescent protein chromophore synthesis revealed by trapped intermediate structures., Barondeau DP, Putnam CD, Kassmann CJ, Tainer JA, Getzoff ED, Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12111-6. Epub 2003 Oct 1. PMID:14523232

Page seeded by OCA on Sun Mar 30 23:20:46 2008

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

OCA

@@ Line 4: / Line 4: @@
 |PDB= 1qyf |SIZE=350|CAPTION= <scene name='initialview01'>1qyf</scene>, resolution 1.50&Aring;
 |SITE=
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>
+|LIGAND= <scene name='pdbligand=CRO:[2-(1-AMINO-2-HYDROXY-PROPYL)-4-(4-HYDROXY-BENZYLIDINE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETALDEHYDE'>CRO</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
 |ACTIVITY=
 |GENE= GFP ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=6100 Aequorea victoria])
+|DOMAIN=
+|RELATEDENTRY=[[1qxt|1QXT]], [[1qy3|1QY3]]
+|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qyf OCA], [http://www.ebi.ac.uk/pdbsum/1qyf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1qyf RCSB]</span>
 }}
@@ Line 27: / Line 30: @@
 [[Category: Putnam, C D.]]
 [[Category: Tainer, J A.]]
-[[Category: EDO]]
-[[Category: MG]]
 [[Category: beta barrel]]
 [[Category: chromophore]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:44:26 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:20:46 2008''