Plasma membrane Ca2+ ATPases are P-type pumps important for intracellular Ca2+ homeostasis. The extreme C termini of alternatively spliced "b"-type Ca2+ pump isoforms resemble those of K+ channels and N-methyl-D-aspartate receptor subunits that interact with channel-clustering proteins of the membrane-associated guanylate kinase (MAGUK) family via PDZ domains, Yeast two-hybrid assays demonstrated strong interaction of Ca2+ pump 4b with the PDZ1+2 domains of several mammalian MAGUKs. Pump 4b and PSD-95 could be co-immunoprecipitated from COS-7 cells overexpressing these proteins. Surface plasmon resonance revealed that a C-terminal pump 4b peptide interacted with the PDZ1+2 domains of hDlg with nanomolar affinity (K-D = 1.6 nm), whereas binding to PDZ3 was in the micromolar range (K-D = 1.2 mu M). In contrast, the corresponding C-terminal peptide of Ca2+ pump 2b interacted weakly with PDZ1+2 and not at all with PDZ3 of hDlg. Ca2+ pump 4b bound strongly to PDZ1+2+3 of hDlg on filter assays, whereas isoform 2b bound weakly, and the splice variants 2a and 4a failed to bind. Together, these data demonstrate a direct physical binding of Ca2+ pump isoform 4b to MAGUKs via their PDZ domains and reveal a novel role of alternative splicing within the family of plasma membrane Ca2+ pumps. Alternative splicing may dictate their specific interaction with PDZ domain-containing proteins, potentially influencing their localization and incorporation into functional multiprotein complexes at the plasma membrane.