7k89

From Proteopedia

(Difference between revisions)

Revision as of 15:19, 18 October 2023

Crystal structure of bovine RPE65 in complex with 4-fluoro-emixustat and palmitate

Structural highlights

7k89 is a 2 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.15Å
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPE65_BOVIN Plays important roles in the production of 11-cis retinal and in visual pigment regeneration. The soluble form binds vitamin A (all-trans-retinol), making it available for LRAT processing to all-trans-retinyl ester. The membrane form, palmitoylated by LRAT, binds all-trans-retinyl esters, making them available for IMH (isomerohydrolase) processing to all-cis-retinol. The soluble form is regenerated by transferring its palmitoyl groups onto 11-cis-retinol, a reaction catalyzed by LRAT. The enzymatic activity is linearly dependent of the expression levels and membrane association.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Recycling of all-trans-retinal to 11-cis-retinal through the visual cycle is a fundamental metabolic pathway in the eye. A potent retinoid isomerase (RPE65) inhibitor, (R)-emixustat, has been developed and tested in several clinical trials; however, it has not received regulatory approval for use in any specific retinopathy. Rapid clearance of this drug presents challenges to maintaining concentrations in eyes within a therapeutic window. To address this pharmacokinetic inadequacy, we rationally designed and synthesized a series of emixustat derivatives with strategically placed fluorine and deuterium atoms to slow down the key metabolic transformations known for emixustat. Crystal structures and quantum chemical analysis of RPE65 in complex with the most potent emixustat derivatives revealed the structural and electronic bases for how fluoro substituents can be favorably accommodated within the active site pocket of RPE65. We found a close ( approximately 3.0 A) F-pi interaction that is predicted to contribute approximately 2.4 kcal/mol to the overall binding energy.

Rational Alteration of Pharmacokinetics of Chiral Fluorinated and Deuterated Derivatives of Emixustat for Retinal Therapy.,Blum E, Zhang J, Zaluski J, Einstein DE, Korshin EE, Kubas A, Gruzman A, Tochtrop GP, Kiser PD, Palczewski K J Med Chem. 2021 Jun 24;64(12):8287-8302. doi: 10.1021/acs.jmedchem.1c00279. Epub, 2021 Jun 3. PMID:34081480^[4]

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

References

↑ Jin M, Li S, Moghrabi WN, Sun H, Travis GH. Rpe65 is the retinoid isomerase in bovine retinal pigment epithelium. Cell. 2005 Aug 12;122(3):449-59. PMID:16096063 doi:10.1016/j.cell.2005.06.042
↑ Kiser PD, Golczak M, Lodowski DT, Chance MR, Palczewski K. Crystal structure of native RPE65, the retinoid isomerase of the visual cycle. Proc Natl Acad Sci U S A. 2009 Oct 13;106(41):17325-30. Epub 2009 Oct 5. PMID:19805034
↑ Golczak M, Kiser PD, Lodowski DT, Maeda A, Palczewski K. Importance of membrane structural integrity for RPE65 retinoid isomerization activity. J Biol Chem. 2010 Mar 26;285(13):9667-82. Epub 2010 Jan 25. PMID:20100834 doi:10.1074/jbc.M109.063941
↑ Blum E, Zhang J, Zaluski J, Einstein DE, Korshin EE, Kubas A, Gruzman A, Tochtrop GP, Kiser PD, Palczewski K. Rational Alteration of Pharmacokinetics of Chiral Fluorinated and Deuterated Derivatives of Emixustat for Retinal Therapy. J Med Chem. 2021 Jun 24;64(12):8287-8302. doi: 10.1021/acs.jmedchem.1c00279. Epub, 2021 Jun 3. PMID:34081480 doi:http://dx.doi.org/10.1021/acs.jmedchem.1c00279

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/7k89"

Categories: Bos taurus | Large Structures | Kiser PD

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[7k89]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7K89 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7K89 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=W4J:(1R)-3-amino-1-[3-(cyclohexylmethoxy)-4-fluorophenyl]propan-1-ol'>W4J</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]] 2.15&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=W4J:(1R)-3-amino-1-[3-(cyclohexylmethoxy)-4-fluorophenyl]propan-1-ol'>W4J</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=7k89 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7k89 OCA], [https://pdbe.org/7k89 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7k89 RCSB], [https://www.ebi.ac.uk/pdbsum/7k89 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7k89 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/RPE65_BOVIN RPE65_BOVIN]] Plays important roles in the production of 11-cis retinal and in visual pigment regeneration. The soluble form binds vitamin A (all-trans-retinol), making it available for LRAT processing to all-trans-retinyl ester. The membrane form, palmitoylated by LRAT, binds all-trans-retinyl esters, making them available for IMH (isomerohydrolase) processing to all-cis-retinol. The soluble form is regenerated by transferring its palmitoyl groups onto 11-cis-retinol, a reaction catalyzed by LRAT. The enzymatic activity is linearly dependent of the expression levels and membrane association.<ref>PMID:16096063</ref> <ref>PMID:19805034</ref> <ref>PMID:20100834</ref>
+[https://www.uniprot.org/uniprot/RPE65_BOVIN RPE65_BOVIN] Plays important roles in the production of 11-cis retinal and in visual pigment regeneration. The soluble form binds vitamin A (all-trans-retinol), making it available for LRAT processing to all-trans-retinyl ester. The membrane form, palmitoylated by LRAT, binds all-trans-retinyl esters, making them available for IMH (isomerohydrolase) processing to all-cis-retinol. The soluble form is regenerated by transferring its palmitoyl groups onto 11-cis-retinol, a reaction catalyzed by LRAT. The enzymatic activity is linearly dependent of the expression levels and membrane association.<ref>PMID:16096063</ref> <ref>PMID:19805034</ref> <ref>PMID:20100834</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 7k89" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Retinoid isomerohydrolase|Retinoid isomerohydrolase]]
 == References ==
 <references/>
@@ Line 25: / Line 28: @@
 [[Category: Bos taurus]]
 [[Category: Large Structures]]
-[[Category: Kiser, P D]]
+[[Category: Kiser PD]]
-[[Category: Beta-propeller]]
-[[Category: Hydrolase-inhibitor complex]]
-[[Category: Inhibitor]]
-[[Category: Isomerase]]
-[[Category: Isomerohydrolase]]
-[[Category: Non-heme iron]]

7k89

From Proteopedia

Revision as of 15:19, 18 October 2023

Crystal structure of bovine RPE65 in complex with 4-fluoro-emixustat and palmitate

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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