Identification of the Substrate Binding Sites within the Yeast Mitochondrial Citrate Transport Protein

• Published in: The Journal of biological chemistry 2007-06, Vol.282 (23), p.17210-17220
• Main Authors: Ma, Chunlong, Remani, Sreevidya, Sun, Jiakang, Kotaria, Rusudan, Mayor, June A., Walters, D. Eric, Kaplan, Ronald S.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Binding Sites; Carrier Proteins - chemistry; Carrier Proteins - metabolism; Kinetics; Mitochondria - metabolism; Models, Molecular; Molecular Sequence Data; Saccharomyces cerevisiae - metabolism
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M611268200

The objective of the present investigation was to identify the substrate binding site(s) within the yeast mitochondrial citrate transport protein (CTP). Our strategy involved kinetically characterizing 30 single-Cys CTP mutants that we had previously constructed based on their hypothesized importance in the structure-based mechanism of this carrier. As part of these studies, a modified transport assay was developed that permitted, for the first time, the accurate determination of Km values that were elevated >100-fold compared with the Cys-less control value. We identified 10 single-Cys CTP mutants that displayed sharply elevated Km values (i.e. 5 to >300-fold). Each of these mutants displayed Vmax values that were reduced by ≥98% and resultant catalytic efficiencies that were reduced by ≥99.9%. Importantly, superposition of this functional data onto the three-dimensional homology-modeled CTP structure, which we previously had developed, revealed that nine of these ten residues form two topographically distinct clusters. Additional modeling showed that: (i) each cluster is capable of forming numerous hydrogen bonds with citrate and (ii) the two clusters are sufficiently distant from one another such that citrate is unlikely to interact with all of these residues at the same time. We deduced from these findings that the CTP contains at least two citrate binding sites per monomer, which are located at increasing depths within the translocation pathway. The identification of these sites, combined with an initial assessment of the citrate-amino acid side-chain interactions that may occur at these sites, substantially extends our understanding of CTP functioning at the molecular level.