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7rfd

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E. coli peptidyl-prolyl cis-trans isomerase, mutant Phe4Ala Phe27CF3-Phe/Phe98CF3-Phe

Structural highlights

7rfd is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.35Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PPIB_ECOLI PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.

Publication Abstract from PubMed

Fluorine atoms are known to display scalar (19)F-(19)F couplings in nuclear magnetic resonance (NMR) spectra when they are sufficiently close in space for nonbonding orbitals to overlap. We show that fluorinated noncanonical amino acids positioned in the hydrophobic core or on the surface of a protein can be linked by scalar through-space (19)F-(19)F ((TS)JFF) couplings even if the (19)F spins are in the time average separated by more than the van der Waals distance. Using two different aromatic amino acids featuring CF3 groups, O-trifluoromethyl-tyrosine and 4-trifluoromethyl-phenylalanine, we show that (19)F-(19)F TOCSY experiments are sufficiently sensitive to detect (TS)JFF couplings between 2.5 and 5 Hz in the 19 kDa protein PpiB measured on a two-channel 400 MHz NMR spectrometer with a regular room temperature probe. A quantitative J evolution experiment enables the measurement of (TS)JFF coupling constants that are up to five times smaller than the (19)F NMR line width. In addition, a new aminoacyl-tRNA synthetase was identified for genetic encoding of N(6)-(trifluoroacetyl)-l-lysine (TFA-Lys) and (19)F-(19)F TOCSY peaks were observed between two TFA-Lys residues incorporated into the proteins AncCDT-1 and mRFP despite high solvent exposure and flexibility of the TFA-Lys side chains. With the ready availability of systems for site-specific incorporation of fluorinated amino acids into proteins by genetic encoding, (19)F-(19)F interactions offer a straightforward way to probe the spatial proximity of selected sites without any assignments of (1)H NMR resonances.

Through-Space Scalar (19)F-(19)F Couplings between Fluorinated Noncanonical Amino Acids for the Detection of Specific Contacts in Proteins.,Orton HW, Qianzhu H, Abdelkader EH, Habel EI, Tan YJ, Frkic RL, Jackson CJ, Huber T, Otting G J Am Chem Soc. 2021 Nov 24;143(46):19587-19598. doi: 10.1021/jacs.1c10104. Epub, 2021 Nov 15. PMID:34780162^[1]

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

References

↑ Orton HW, Qianzhu H, Abdelkader EH, Habel EI, Tan YJ, Frkic RL, Jackson CJ, Huber T, Otting G. Through-Space Scalar (19)F-(19)F Couplings between Fluorinated Noncanonical Amino Acids for the Detection of Specific Contacts in Proteins. J Am Chem Soc. 2021 Nov 24;143(46):19587-19598. doi: 10.1021/jacs.1c10104. Epub, 2021 Nov 15. PMID:34780162 doi:http://dx.doi.org/10.1021/jacs.1c10104

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7rfd"

Categories: Escherichia coli | Large Structures | Frkic RL | Jackson CJ | Otting G

@@ Line 3: / Line 3: @@
 <StructureSection load='7rfd' size='340' side='right'caption='[[7rfd]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[7rfd]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RFD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[7rfd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7RFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7RFD FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=55I:'>55I</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]] 1.35&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7n3j|7n3j]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=55I:4-(trifluoromethyl)-L-phenylalanine'>55I</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peptidylprolyl_isomerase Peptidylprolyl isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.2.1.8 5.2.1.8] </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=7rfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7rfd OCA], [https://pdbe.org/7rfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7rfd RCSB], [https://www.ebi.ac.uk/pdbsum/7rfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7rfd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/J7QN08_ECOLX J7QN08_ECOLX]] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.[RuleBase:RU363019]
+[https://www.uniprot.org/uniprot/PPIB_ECOLI PPIB_ECOLI] PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 7rfd" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Cyclophilin 3D structures|Cyclophilin 3D structures]]
+*[[Peptidyl-prolyl cis-trans isomerase 3D structures|Peptidyl-prolyl cis-trans isomerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Peptidylprolyl isomerase]]
+[[Category: Frkic RL]]
-[[Category: Frkic, R L]]
+[[Category: Jackson CJ]]
-[[Category: Jackson, C J]]
+[[Category: Otting G]]
-[[Category: Otting, G]]
-[[Category: Isomerase]]
-[[Category: Non-canonical amino acid]]
-[[Category: Peptidyl-prolyl cis-trans isomerase]]
-[[Category: Trifluoromethyl-phenylalanine]]

7rfd

From Proteopedia

Current revision

E. coli peptidyl-prolyl cis-trans isomerase, mutant Phe4Ala Phe27CF3-Phe/Phe98CF3-Phe

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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