The Schizosaccharomyces pombe gene, fkp39(+), encoding a homolog of FKBP(FK506 binding protein)-type peptidyl prolyl cis-trans isomerase (PPIase), was isolated and the primary structure was determined. This gene product (SpFkbp39p) showed PPIase enzymatic activity in a chymotrypsin-dependent enzyme assay involving recombinant SpFkbp39p. Comparison of the primary structures of the catalytic domains of FKBPs, including SpFkbp39p, revealed that FKBPs could be classified into four groups. This categorization corresponding to the known subcellular localization of the FKBPs, makes the prediction of the subcellular localization of FKBPs based on their primary structures feasible. SpFkbp39p was considered to be a member of the nuclear-type FKBP group from this relationship between primary structure and subcellular localization. An immunofluorescence assay against HA-epitope-tagged SpFkbp39p revealed that SpFkbp39p is localized to the nucleus, as predicted. Residues conserved in a "group-specific" manner in the catalytic domain were mapped to their corresponding three-dimensional positions; these "group-specific" residues were located in close proximity in distinct regions mostly on the protein surface, which implies the presence of "group-specific" regulatory functional regions. We also found that nuclear-type FKBPs, including SpFkbp39p, have two highly conserved domains other than catalytic ones, with further basic and acidic charged regions, especially in the case of nuclear-type FKBPs. This is the first report indicating that there is a rule for the relationship between the subcellular localization and structure of the catalytic domain of a FKBP.