4EP9

CRYSTAL STRUCTURE OF RAT CARNITINE PALMITOYLTRANSFERASE 2 IN COMPLEX WITH CoA-site inhibitor

Summary for 4EP9

• Entry DOI: 10.2210/pdb4ep9/pdb
• Related: 2DEB 2FW3 2FYO 2H4T 2RCU 4EPH
• Descriptor: Carnitine O-palmitoyltransferase 2, mitochondrial, 4-[({1-[(5-chloro-2-methoxyphenyl)sulfonyl]-4-methyl-2,3-dihydro-1H-indol-6-yl}carbonyl)amino]benzoic acid, PALMITIC ACID, ... (4 entities in total)
• Functional Keywords: transferase, acyltransferase, mitochondrial protein, coa, acylcarnitine, mitochondrial inner membrane, lipid transport, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Rattus norvegicus (brown rat,rat,rats)
• Cellular location: Mitochondrion inner membrane ; Peripheral membrane protein ; Matrix side : P18886
• Total number of polymer chains: 1
• Total formula weight: 74323.47

Authors

Rufer, A.C.,Thoma, R.,Benz, J.,Stihle, M.,Gsell, B.,De Roo, E.,Banner, D.W.,Mueller, F.,Chomienne, O.,Hennig, M. (deposition date: 2012-04-17, release date: 2013-04-17, Last modification date: 2023-09-13)

Primary citation

Perspicace, S.,Rufer, A.C.,Thoma, R.,Mueller, F.,Hennig, M.,Ceccarelli, S.,Schulz-Gasch, T.,Seelig, J.
Isothermal titration calorimetry with micelles: Thermodynamics of inhibitor binding to carnitine palmitoyltransferase 2 membrane protein.
FEBS Open Bio, 3:204-211, 2013

PubMed Abstract: Carnitine palmitoyl transferase 2 (CPT-2) is a key enzyme in the mitochondrial fatty acid metabolism. The active site is comprised of a Y-shaped tunnel with distinct binding sites for the substrate acylcarnitine and the cofactor CoA. We investigated the thermodynamics of binding of four inhibitors directed against either the CoA or the acylcarnitine binding sites using isothermal titration calorimetry (ITC). CPT-2 is a monotopic membrane protein and was solubilized by β-octylglucoside (β-OG) above its critical micellar concentration (CMC) to perform inhibitor titrations in solutions containing detergent micelles. The CMC of β-OG in the presence of inhibitors was measured with ITC and small variations were observed. The inhibitors bound to rat CPT-2 (rCPT-2) with 1:1 stoichiometry and the dissociation constants were in the range of K D = 2-20 μM. New X-ray structures and docking models of rCPT-2 in complex with inhibitors enable an analysis of the thermodynamic data in the context of the interaction observed for the individual binding sites of the ligands. For all ligands the binding enthalpy was exothermic, and enthalpy as well as entropy contributed to the binding reaction, with the exception of ST1326 for which binding was solely enthalpy-driven. The substrate analog ST1326 binds to the acylcarnitine binding site and a heat capacity change close to zero suggests a balance of electrostatic and hydrophobic interactions. An excellent correlation of the thermodynamic (ITC) and structural (X-ray crystallography, models) data was observed suggesting that ITC measurements provide valuable information for optimizing inhibitor binding in drug discovery.

PubMed: 23772395
DOI: 10.1016/j.fob.2013.04.003

Experimental method

X-RAY DIFFRACTION (2.03 Å)